SERVER-27549 Print message on intentional server crash.

94 files changed, 226 insertions, 229 deletions

diff --git a/buildscripts/resmokeconfig/suites/disk_mmapv1.yml b/buildscripts/resmokeconfig/suites/disk_mmapv1.yml
index 6fb993c8a4b..194e5121cf9 100644
--- a/buildscripts/resmokeconfig/suites/disk_mmapv1.yml
+++ b/buildscripts/resmokeconfig/suites/disk_mmapv1.yml
@@ -4,6 +4,10 @@ selector:
     - jstests/disk/*.js
     exclude_files:
     - jstests/disk/repair2.js  # SERVER-18256
+    # The following tests require a dedicated disk partition to be set up. Otherwise they will
+    # silently be no-ops.
+    - jstests/disk/repair3.js
+    - jstests/disk/repair4.js
 
 executor:
   js_test:
diff --git a/jstests/auth/access_control_with_unreachable_configs.js b/jstests/auth/access_control_with_unreachable_configs.js
index 7e173475f7a..3d7f9ab24a6 100644
--- a/jstests/auth/access_control_with_unreachable_configs.js
+++ b/jstests/auth/access_control_with_unreachable_configs.js
@@ -36,7 +36,7 @@ assert.commandWorked(db.adminCommand('serverStatus'));
 jsTest.log('repeat without config server');
 
 // shut down only config server
-MongoRunner.stopMongod(config.port, /*signal*/ 15);
+MongoRunner.stopMongod(config);
 
 // open a new connection to mongos (unauthorized)
 var conn2 = new Mongo(mongos.host);
diff --git a/jstests/auth/authz_modifications_access_control.js b/jstests/auth/authz_modifications_access_control.js
index 7f7b01e12ba..483a54be4f8 100644
--- a/jstests/auth/authz_modifications_access_control.js
+++ b/jstests/auth/authz_modifications_access_control.js
@@ -296,7 +296,7 @@ function runTest(conn) {
 jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({auth: ''});
 runTest(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/basic_role_auth.js b/jstests/auth/basic_role_auth.js
index 0dfef842da8..a2484565755 100644
--- a/jstests/auth/basic_role_auth.js
+++ b/jstests/auth/basic_role_auth.js
@@ -486,7 +486,7 @@ var runTests = function(conn) {
 
 var conn = MongoRunner.runMongod({auth: ''});
 runTests(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 1, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/clac_system_colls.js b/jstests/auth/clac_system_colls.js
index 26a315db252..3ac67e28291 100644
--- a/jstests/auth/clac_system_colls.js
+++ b/jstests/auth/clac_system_colls.js
@@ -57,7 +57,7 @@ function runTest(admindb) {
 jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({auth: ''});
 runTest(conn.getDB("admin"));
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/copyauth.js b/jstests/auth/copyauth.js
index 6960692ef24..d93e726eaa1 100644
--- a/jstests/auth/copyauth.js
+++ b/jstests/auth/copyauth.js
@@ -78,7 +78,7 @@ function ClusterSpawnHelper(clusterType, startWithAuth, startWithTransitionToAut
         } else if (clusterType === "repl") {
             replSetTest.stopSet();
         } else {
-            MongoRunner.stopMongod(this.conn.port);
+            MongoRunner.stopMongod(this.conn);
         }
     };
 }
diff --git a/jstests/auth/getMore.js b/jstests/auth/getMore.js
index ba1dc19173b..d8795278cbc 100644
--- a/jstests/auth/getMore.js
+++ b/jstests/auth/getMore.js
@@ -226,9 +226,9 @@
     }
 
     // Run the test on a standalone.
-    let mongod = MongoRunner.runMongod({auth: "", bind_ip: "127.0.0.1"});
-    runTest(mongod);
-    MongoRunner.stopMongod(mongod);
+    let conn = MongoRunner.runMongod({auth: "", bind_ip: "127.0.0.1"});
+    runTest(conn);
+    MongoRunner.stopMongod(conn);
 
     // Run the test on a sharded cluster.
     let cluster = new ShardingTest(
diff --git a/jstests/auth/killop_own_ops.js b/jstests/auth/killop_own_ops.js
index d412e31c8ce..562ee2645b4 100644
--- a/jstests/auth/killop_own_ops.js
+++ b/jstests/auth/killop_own_ops.js
@@ -149,9 +149,9 @@
         assert.lt(diff, 30000, "Start: " + start + "; end: " + end + "; diff: " + diff);
     }
 
-    var m = MongoRunner.runMongod({auth: ""});
-    runTest(m);
-    MongoRunner.stopMongod(m);
+    var conn = MongoRunner.runMongod({auth: ""});
+    runTest(conn);
+    MongoRunner.stopMongod(conn);
 
     // TODO: This feature is currently not supported on sharded clusters.
     /*var st =
diff --git a/jstests/auth/localhostAuthBypass.js b/jstests/auth/localhostAuthBypass.js
index cd56e3bc160..aeb11465596 100644
--- a/jstests/auth/localhostAuthBypass.js
+++ b/jstests/auth/localhostAuthBypass.js
@@ -120,7 +120,7 @@ var authenticate = function(mongo) {
 
 var shutdown = function(conn) {
     print("============ shutting down.");
-    MongoRunner.stopMongod(conn.port, /*signal*/ false, {auth: {user: username, pwd: password}});
+    MongoRunner.stopMongod(conn, /*signal*/ false, {auth: {user: username, pwd: password}});
 };
 
 var runTest = function(useHostName) {
diff --git a/jstests/auth/log_user_basic.js b/jstests/auth/log_user_basic.js
index 9e782fed9f5..298aa1f2eb5 100644
--- a/jstests/auth/log_user_basic.js
+++ b/jstests/auth/log_user_basic.js
@@ -248,9 +248,9 @@ if (0) {
         })();
     };
 
-    var mongo = MongoRunner.runMongod({verbose: 5, setParameter: 'logUserIds=1'});
-    doTest(mongo, new Mongo(mongo.host));
-    MongoRunner.stopMongod(mongo.port);
+    var conn = MongoRunner.runMongod({verbose: 5, setParameter: 'logUserIds=1'});
+    doTest(conn, new Mongo(conn.host));
+    MongoRunner.stopMongod(conn);
 
     var st = new ShardingTest(
         {shards: 1, verbose: 5, other: {mongosOptions: {setParameter: 'logUserIds=1'}}});
diff --git a/jstests/auth/log_userid_off.js b/jstests/auth/log_userid_off.js
index 62d0af74c02..23e90b6fd1e 100644
--- a/jstests/auth/log_userid_off.js
+++ b/jstests/auth/log_userid_off.js
@@ -32,7 +32,7 @@ var doTest = function(mongo, callSetParam) {
 
 var mongo = MongoRunner.runMongod({verbose: 5});
 doTest(mongo);
-MongoRunner.stopMongod(mongo.port);
+MongoRunner.stopMongod(mongo);
 
 var st = new ShardingTest({shards: 1, verbose: 5});
 doTest(st.s);
diff --git a/jstests/auth/mergeAuthCollsCommand.js b/jstests/auth/mergeAuthCollsCommand.js
index c89a7ff460d..d5084d76a85 100644
--- a/jstests/auth/mergeAuthCollsCommand.js
+++ b/jstests/auth/mergeAuthCollsCommand.js
@@ -117,7 +117,7 @@ function runTest(conn) {
 jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({});
 runTest(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3});
diff --git a/jstests/auth/pseudo_commands.js b/jstests/auth/pseudo_commands.js
index 2a882f219c8..921c1c3f548 100644
--- a/jstests/auth/pseudo_commands.js
+++ b/jstests/auth/pseudo_commands.js
@@ -187,7 +187,7 @@ function runTest(conn) {
 jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({auth: ''});
 runTest(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/role_management_commands_edge_cases.js b/jstests/auth/role_management_commands_edge_cases.js
index 5af309a1a7a..8adb7571692 100644
--- a/jstests/auth/role_management_commands_edge_cases.js
+++ b/jstests/auth/role_management_commands_edge_cases.js
@@ -376,7 +376,7 @@ function runTest(conn) {
 jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({auth: ''});
 runTest(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/role_management_commands_standalone.js b/jstests/auth/role_management_commands_standalone.js
index 38f848f9936..d35f2c30a3f 100644
--- a/jstests/auth/role_management_commands_standalone.js
+++ b/jstests/auth/role_management_commands_standalone.js
@@ -5,5 +5,5 @@
 
     var conn = MongoRunner.runMongod({auth: '', useHostname: false});
     runAllRoleManagementCommandsTests(conn);
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 })();
diff --git a/jstests/auth/server-4892.js b/jstests/auth/server-4892.js
index a6bbf89e69e..bfa51347fe1 100644
--- a/jstests/auth/server-4892.js
+++ b/jstests/auth/server-4892.js
@@ -28,7 +28,7 @@ function withMongod(extraMongodArgs, operation) {
     try {
         operation(mongod);
     } finally {
-        MongoRunner.stopMongod(mongod.port);
+        MongoRunner.stopMongod(mongod);
     }
 }
 
diff --git a/jstests/auth/user_defined_roles.js b/jstests/auth/user_defined_roles.js
index c786018dbb5..8c480385369 100644
--- a/jstests/auth/user_defined_roles.js
+++ b/jstests/auth/user_defined_roles.js
@@ -142,7 +142,7 @@ function runTest(conn) {
 jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({auth: ''});
 runTest(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/user_management_commands_edge_cases.js b/jstests/auth/user_management_commands_edge_cases.js
index ab42714fb9a..704043e24b3 100644
--- a/jstests/auth/user_management_commands_edge_cases.js
+++ b/jstests/auth/user_management_commands_edge_cases.js
@@ -279,7 +279,7 @@ jsTest.log('Test standalone');
 var conn = MongoRunner.runMongod({auth: ''});
 conn.getDB('admin').runCommand({setParameter: 1, newCollectionsUsePowerOf2Sizes: false});
 runTest(conn);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log('Test sharding');
 var st = new ShardingTest({shards: 2, config: 3, keyFile: 'jstests/libs/key1'});
diff --git a/jstests/auth/user_management_commands_standalone.js b/jstests/auth/user_management_commands_standalone.js
index 951ee1e9801..192f5968aa2 100644
--- a/jstests/auth/user_management_commands_standalone.js
+++ b/jstests/auth/user_management_commands_standalone.js
@@ -5,5 +5,5 @@
 
     var conn = MongoRunner.runMongod({auth: '', useHostname: false});
     runAllUserManagementCommandsTests(conn);
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 })();
diff --git a/jstests/disk/repair.js b/jstests/disk/repair.js
index cf86e50434d..e8c39f9563c 100644
--- a/jstests/disk/repair.js
+++ b/jstests/disk/repair.js
@@ -27,7 +27,7 @@ function check() {
     assert.eq.automsg("1", "db[ baseName ].count()");
 }
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 resetDbpath(repairpath);
 m = MongoRunner.runMongod({
@@ -38,7 +38,7 @@ m = MongoRunner.runMongod({
 db = m.getDB(baseName);
 assert.commandWorked(db.runCommand({repairDatabase: 1}));
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 resetDbpath(repairpath);
 rc = runMongoProgram(
@@ -51,7 +51,7 @@ m = MongoRunner.runMongod({
 });
 db = m.getDB(baseName);
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 resetDbpath(repairpath);
 rc = runMongoProgram("mongod", "--repair", "--port", m.port, "--dbpath", dbpath);
diff --git a/jstests/disk/repair2.js b/jstests/disk/repair2.js
index a73194c15eb..11be561ef71 100644
--- a/jstests/disk/repair2.js
+++ b/jstests/disk/repair2.js
@@ -48,7 +48,7 @@ for (f in files) {
 assert(fileCount > 0, "Expected more than zero nondirectory files in the database directory");
 
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 resetDbpath(repairpath);
 m = MongoRunner.runMongod({
@@ -60,7 +60,7 @@ m = MongoRunner.runMongod({
 db = m.getDB(baseName);
 assert.commandWorked(db.runCommand({repairDatabase: 1}));
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 // Test long database names
 resetDbpath(repairpath);
@@ -73,7 +73,7 @@ m = MongoRunner.runMongod({
 db = m.getDB(longDBName);
 assert.writeOK(db[baseName].save({}));
 assert.commandWorked(db.runCommand({repairDatabase: 1}));
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 // Test long repairPath
 resetDbpath(longRepairPath);
@@ -87,7 +87,7 @@ m = MongoRunner.runMongod({
 db = m.getDB(longDBName);
 assert.commandWorked(db.runCommand({repairDatabase: 1, backupOriginalFiles: true}));
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 // Test database name and repairPath with --repair
 resetDbpath(longRepairPath);
@@ -109,7 +109,7 @@ m = MongoRunner.runMongod({
 });
 db = m.getDB(longDBName);
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 resetDbpath(repairpath);
 returnCode = runMongoProgram("mongod",
@@ -131,7 +131,7 @@ m = MongoRunner.runMongod({
 });
 db = m.getDB(baseName);
 check();
-MongoRunner.stopMongod(m.port);
+MongoRunner.stopMongod(m);
 
 resetDbpath(repairpath);
 returnCode =
diff --git a/jstests/disk/repair3.js b/jstests/disk/repair3.js
index a2b64282d99..f339a666a70 100644
--- a/jstests/disk/repair3.js
+++ b/jstests/disk/repair3.js
@@ -47,7 +47,7 @@ if (doIt) {
     }
 
     check();
-    MongoRunner.stopMongod(m.port);
+    MongoRunner.stopMongod(m);
 
     resetDbpath(repairpath);
     var rc = runMongoProgram("mongod",
@@ -73,5 +73,5 @@ if (doIt) {
     });
     db = m.getDB(baseName);
     check();
-    MongoRunner.stopMongod(m.port);
+    MongoRunner.stopMongod(m);
 }
diff --git a/jstests/disk/repair4.js b/jstests/disk/repair4.js
index 2fed96e3674..15033dc5986 100644
--- a/jstests/disk/repair4.js
+++ b/jstests/disk/repair4.js
@@ -49,5 +49,5 @@ if (doIt) {
     }
 
     check();
-    MongoRunner.stopMongod(port);
+    MongoRunner.stopMongod(m);
 }
diff --git a/jstests/dur/a_quick.js b/jstests/dur/a_quick.js
index 5e1ff17a758..1528d6a8452 100644
--- a/jstests/dur/a_quick.js
+++ b/jstests/dur/a_quick.js
@@ -83,7 +83,7 @@ sleep(8000);
 
 // kill the process hard
 tst.log("kill -9 mongod");
-MongoRunner.stopMongod(conn.port, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 
diff --git a/jstests/dur/checksum.js b/jstests/dur/checksum.js
index 0076024de66..789bae418ec 100644
--- a/jstests/dur/checksum.js
+++ b/jstests/dur/checksum.js
@@ -3,27 +3,6 @@
 var testname = "dur_checksum";
 var path = MongoRunner.dataPath + testname;
 
-if (0) {
-    // This is used to create the prototype journal file.
-    jsTest.log("Just creating prototype journal, not testing anything");
-    var conn = MongoRunner.runMongod({dbpath: path, journal: ""});
-    var db = conn.getDB("test");
-
-    // each insert is in it's own commit.
-    db.foo.insert({a: 1});
-    db.runCommand({getlasterror: 1, j: 1});
-
-    db.foo.insert({a: 2});
-    db.runCommand({getlasterror: 1, j: 1});
-
-    MongoRunner.stopMongod(conn.port, /*signal*/ 9);
-
-    jsTest.log("Journal file left at " + path + "/journal/j._0");
-    quit();
-    // A hex editor must be used to replace the checksums of specific journal sections with
-    // "0BADC0DE 1BADC0DE 2BADC0DE 3BADCD0E"
-}
-
 function startMongodWithJournal() {
     return MongoRunner.runMongod({
         restart: true,
@@ -42,7 +21,7 @@ copyFile("jstests/libs/dur_checksum_good.journal", path + "/journal/j._0");
 var conn = startMongodWithJournal();
 var db = conn.getDB('test');
 assert.eq(db.foo.count(), 2);
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 // dur_checksum_bad_last.journal is good.journal with the bad checksum on the last section.
 jsTest.log("Starting with bad_last.journal");
@@ -52,7 +31,7 @@ copyFile("jstests/libs/dur_checksum_bad_last.journal", path + "/journal/j._0");
 conn = startMongodWithJournal();
 var db = conn.getDB('test');
 assert.eq(db.foo.count(), 1);  // 2nd insert "never happened"
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 // dur_checksum_bad_first.journal is good.journal with the bad checksum on the prior section.
 // This means there is a good commit after the bad one. We currently ignore this, but a future
@@ -64,7 +43,7 @@ copyFile("jstests/libs/dur_checksum_bad_first.journal", path + "/journal/j._0");
 conn = startMongodWithJournal();
 var db = conn.getDB('test');
 assert.eq(db.foo.count(), 0);  // Neither insert happened.
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 // If we detect an error in a non-final journal file, that is considered an error.
 jsTest.log("Starting with bad_last.journal followed by good.journal");
diff --git a/jstests/dur/dropdb.js b/jstests/dur/dropdb.js
index 9d60f60869a..d79c9b60ab8 100644
--- a/jstests/dur/dropdb.js
+++ b/jstests/dur/dropdb.js
@@ -125,7 +125,7 @@ verify();
 
 // kill the process hard
 log("kill 9");
-MongoRunner.stopMongod(conn.port, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 
diff --git a/jstests/dur/dur1.js b/jstests/dur/dur1.js
index 568ba4ada55..3bd77e42c54 100644
--- a/jstests/dur/dur1.js
+++ b/jstests/dur/dur1.js
@@ -111,7 +111,7 @@ printjson(conn.getDB('admin').runCommand({getlasterror: 1, fsync: 1}));
 
 // kill the process hard
 log("kill 9");
-MongoRunner.stopMongod(conn.port, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 
diff --git a/jstests/dur/dur1_tool.js b/jstests/dur/dur1_tool.js
index e96e1f20c6d..fa645fac11f 100644
--- a/jstests/dur/dur1_tool.js
+++ b/jstests/dur/dur1_tool.js
@@ -111,7 +111,7 @@ printjson(conn.getDB('admin').runCommand({getlasterror: 1, fsync: 1}));
 
 // kill the process hard
 log("kill 9");
-MongoRunner.stopMongod(conn, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 
diff --git a/jstests/dur/dur2.js b/jstests/dur/dur2.js
index 5ff6aa9840e..b56949e00ad 100644
--- a/jstests/dur/dur2.js
+++ b/jstests/dur/dur2.js
@@ -82,7 +82,7 @@ conn = MongoRunner.runMongod({
 work();
 
 log("kill -9");
-MongoRunner.stopMongod(conn, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 assert(listFiles(path + "/journal/").length > 0,
diff --git a/jstests/dur/lsn.js b/jstests/dur/lsn.js
index 679475ad6ea..497b4597b2e 100644
--- a/jstests/dur/lsn.js
+++ b/jstests/dur/lsn.js
@@ -94,7 +94,7 @@ log("wait a while for a sync and an lsn write");
 sleep(14);  // wait for lsn write
 
 log("kill mongod -9");
-MongoRunner.stopMongod(conn, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 
diff --git a/jstests/dur/manyRestart.js b/jstests/dur/manyRestart.js
index f4d03f60edc..76c658d7bdd 100644
--- a/jstests/dur/manyRestart.js
+++ b/jstests/dur/manyRestart.js
@@ -146,7 +146,7 @@ for (var i = 0; i < 3; ++i) {
 
     // kill the process hard
     log("hard kill");
-    MongoRunner.stopMongod(conn, /*signal*/ 9);
+    MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     sleep(5000);
 }
@@ -204,7 +204,7 @@ for (var i = 0; i < 5; ++i) {
 
     // kill the process hard
     log("hard kill");
-    MongoRunner.stopMongod(conn, /*signal*/ 9);
+    MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     sleep(5000);
 }
diff --git a/jstests/dur/oplog.js b/jstests/dur/oplog.js
index be0bdd17948..fb56455c193 100644
--- a/jstests/dur/oplog.js
+++ b/jstests/dur/oplog.js
@@ -127,7 +127,7 @@ work();
 printjson(conn.getDB('admin').runCommand({getlasterror: 1, fsync: 1}));
 
 // kill the process hard
-MongoRunner.stopMongod(conn, /*signal*/ 9);
+MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
 // journal file should be present, and non-empty as we killed hard
 
diff --git a/jstests/fail_point/fail_point.js b/jstests/fail_point/fail_point.js
index 0bb08f0b358..b8c877cb9b2 100644
--- a/jstests/fail_point/fail_point.js
+++ b/jstests/fail_point/fail_point.js
@@ -69,7 +69,7 @@ var runTest = function(adminDB) {
 
 var conn = MongoRunner.runMongod();
 runTest(conn.getDB('admin'));
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 ///////////////////////////////////////////////////////////
 // Test mongos
diff --git a/jstests/libs/command_line/test_parsed_options.js b/jstests/libs/command_line/test_parsed_options.js
index c38d07668af..50e2733c520 100644
--- a/jstests/libs/command_line/test_parsed_options.js
+++ b/jstests/libs/command_line/test_parsed_options.js
@@ -52,7 +52,7 @@ function testGetCmdLineOptsMongod(mongoRunnerConfig, expectedResult) {
         var getCmdLineOptsBaseMongod = baseMongod.adminCommand("getCmdLineOpts");
 
         // Stop the mongod we used to get the options
-        MongoRunner.stopMongod(baseMongod.port);
+        MongoRunner.stopMongod(baseMongod);
 
         return getCmdLineOptsBaseMongod;
     }
@@ -114,7 +114,7 @@ function testGetCmdLineOptsMongod(mongoRunnerConfig, expectedResult) {
 
     // Cleanup
     mongod.getDB("admin").logout();
-    MongoRunner.stopMongod(mongod.port);
+    MongoRunner.stopMongod(mongod);
 }
 
 // Test that the parsed result of setting certain command line options has the correct format in
diff --git a/jstests/libs/ssl_test.js b/jstests/libs/ssl_test.js
index 11874ebc01e..1d3c2b06fe0 100644
--- a/jstests/libs/ssl_test.js
+++ b/jstests/libs/ssl_test.js
@@ -74,7 +74,8 @@ SSLTest.prototype.connectWorked = function() {
     var serverPID = _startMongoProgram.apply(null, serverArgv);
     try {
         assert.soon(function() {
-            return checkProgram(serverPID) && (0 === _runMongoProgram.apply(null, clientArgv));
+            return checkProgram(serverPID).alive &&
+                (0 === _runMongoProgram.apply(null, clientArgv));
         }, "connect failed", connectTimeoutMillis);
     } catch (ex) {
         return false;
diff --git a/jstests/multiVersion/libs/dumprestore_helpers.js b/jstests/multiVersion/libs/dumprestore_helpers.js
index 5502a10bbb9..c62c817332b 100644
--- a/jstests/multiVersion/libs/dumprestore_helpers.js
+++ b/jstests/multiVersion/libs/dumprestore_helpers.js
@@ -95,7 +95,7 @@ function multiVersionDumpRestoreTest(configObj) {
             host: serverSource.host,
             db: testBaseName
         });
-        MongoRunner.stopMongod(serverSource.port);
+        MongoRunner.stopMongod(serverSource);
     } else { /* "mongos" */
         MongoRunner.runMongoTool("mongodump", {
             out: configObj.dumpDir,
@@ -161,7 +161,7 @@ function multiVersionDumpRestoreTest(configObj) {
     if (configObj.restoreType === "mongos") {
         shardingTest.stop();
     } else {
-        MongoRunner.stopMongod(serverDest.port);
+        MongoRunner.stopMongod(serverDest);
     }
 }
 
diff --git a/jstests/multiVersion/transitioning_to_and_from_WT.js b/jstests/multiVersion/transitioning_to_and_from_WT.js
index f51e21a2ef9..682abc95cfa 100644
--- a/jstests/multiVersion/transitioning_to_and_from_WT.js
+++ b/jstests/multiVersion/transitioning_to_and_from_WT.js
@@ -121,7 +121,7 @@
         assert.eq(0, ret);
 
         // stop previous mongod
-        MongoRunner.stopMongod(toolTest.port);
+        MongoRunner.stopMongod(toolTest.m);
 
         // clear old node configuration info
         toolTest.m = null;
diff --git a/jstests/noPassthrough/compression_options.js b/jstests/noPassthrough/compression_options.js
index acbb1d66ba7..3dc4e3b5601 100644
--- a/jstests/noPassthrough/compression_options.js
+++ b/jstests/noPassthrough/compression_options.js
@@ -32,7 +32,7 @@
         output = JSON.parse(output);
 
         assert.eq(output.compression, expected);
-        MongoRunner.stopMongod(mongo.port);
+        MongoRunner.stopMongod(mongo);
     };
 
     assert.isnull(MongoRunner.runMongod({networkMessageCompressors: "snappy,disabled"}));
diff --git a/jstests/noPassthrough/dir_per_db_and_split.js b/jstests/noPassthrough/dir_per_db_and_split.js
index a9ddb0eb6d0..2704afa4aa2 100644
--- a/jstests/noPassthrough/dir_per_db_and_split.js
+++ b/jstests/noPassthrough/dir_per_db_and_split.js
@@ -13,7 +13,7 @@ if (!jsTest.options().storageEngine || jsTest.options().storageEngine === "wired
     assert(listFiles(dbpath + "/foo/index").length > 0);
     assert(listFiles(dbpath + "/foo/collection").length > 0);
 
-    MongoRunner.stopMongod(m.port);
+    MongoRunner.stopMongod(m);
 
     // Subsequent attempts to start server using same dbpath but different
     // wiredTigerDirectoryForIndexes and directoryperdb options should fail.
diff --git a/jstests/noPassthrough/directoryperdb.js b/jstests/noPassthrough/directoryperdb.js
index 52d3d700006..8561b810156 100644
--- a/jstests/noPassthrough/directoryperdb.js
+++ b/jstests/noPassthrough/directoryperdb.js
@@ -39,7 +39,7 @@
     files = listFiles(files[0].name);
     assert(files.length > 0);
 
-    MongoRunner.stopMongod(m.port);
+    MongoRunner.stopMongod(m);
 
     // Subsequent attempt to start server using same dbpath without directoryperdb should fail.
     assert.isnull(MongoRunner.runMongod({dbpath: dbpath, restart: true}));
diff --git a/jstests/noPassthrough/durable_view_catalog.js b/jstests/noPassthrough/durable_view_catalog.js
index 5c06cf31167..02afd804fda 100644
--- a/jstests/noPassthrough/durable_view_catalog.js
+++ b/jstests/noPassthrough/durable_view_catalog.js
@@ -32,7 +32,7 @@
     assert.commandWorked(viewsDB.runCommand({drop: "view1", writeConcern: {j: 1}}));
 
     // Hard kill the mongod to ensure the data was indeed synced to durable storage.
-    MongoRunner.stopMongod(conn, 9);
+    MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     // Restart the mongod.
     conn = MongoRunner.runMongod(mongodArgs);
diff --git a/jstests/noPassthrough/exit_logging.js b/jstests/noPassthrough/exit_logging.js
index f996766866f..1dee8c347db 100644
--- a/jstests/noPassthrough/exit_logging.js
+++ b/jstests/noPassthrough/exit_logging.js
@@ -48,7 +48,7 @@
             crashFn(conn);
             checkOutput();
         } finally {
-            launcher.stop(conn, undefined, {allowedExitCodes: [expectedExitCode]});
+            launcher.stop(conn, undefined, {allowedExitCode: expectedExitCode});
         }
     }
 
diff --git a/jstests/noPassthrough/index_no_retry.js b/jstests/noPassthrough/index_no_retry.js
index e05881c590a..40442555760 100644
--- a/jstests/noPassthrough/index_no_retry.js
+++ b/jstests/noPassthrough/index_no_retry.js
@@ -60,5 +60,5 @@
     var indexes = t.getIndexes();
     assert.eq(1, indexes.length, 'unfinished indexes in listIndexes result: ' + tojson(indexes));
 
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 }());
diff --git a/jstests/noPassthrough/index_retry.js b/jstests/noPassthrough/index_retry.js
index 4c870eacb10..f546c81ec38 100644
--- a/jstests/noPassthrough/index_retry.js
+++ b/jstests/noPassthrough/index_retry.js
@@ -61,5 +61,5 @@
               indexes.length,
               'unexpected number of indexes in listIndexes result: ' + tojson(indexes));
 
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 }());
diff --git a/jstests/noPassthrough/libs/backup_restore.js b/jstests/noPassthrough/libs/backup_restore.js
index 29380a1ef05..cba8915aec1 100644
--- a/jstests/noPassthrough/libs/backup_restore.js
+++ b/jstests/noPassthrough/libs/backup_restore.js
@@ -347,9 +347,16 @@ var BackupRestoreTest = function(options) {
         rst.waitForState(hiddenNode, [ReplSetTest.State.RECOVERING, ReplSetTest.State.SECONDARY]);
 
         // Stop CRUD client and FSM client.
-        assert(checkProgram(crudPid), testName + ' CRUD client was not running at end of test');
-        assert(checkProgram(fsmPid), testName + ' FSM client was not running at end of test');
+        var crudStatus = checkProgram(crudPid);
+        assert(crudStatus.alive,
+               testName + ' CRUD client was not running at end of test and exited with code: ' +
+                   crudStatus.exitCode);
         stopMongoProgramByPid(crudPid);
+
+        var fsmStatus = checkProgram(fsmPid);
+        assert(fsmStatus.alive,
+               testName + ' FSM client was not running at end of test and exited with code: ' +
+                   fsmStatus.exitCode);
         stopMongoProgramByPid(fsmPid);
 
         // Wait up to 5 minutes until the new hidden node is in state SECONDARY.
diff --git a/jstests/noPassthrough/minvalid2.js b/jstests/noPassthrough/minvalid2.js
index f41a6a7e369..f51a1430490 100644
--- a/jstests/noPassthrough/minvalid2.js
+++ b/jstests/noPassthrough/minvalid2.js
@@ -90,4 +90,4 @@ assert.soon(function() {
         'it does not contain the necessary operations for us to reach a consistent state');
 });
 
-replTest.stopSet(undefined, undefined, {allowedExitCodes: [MongoRunner.EXIT_ABRUPT]});
+replTest.stopSet();
diff --git a/jstests/noPassthrough/parameters.js b/jstests/noPassthrough/parameters.js
index 53fe45acf7d..e157497464b 100644
--- a/jstests/noPassthrough/parameters.js
+++ b/jstests/noPassthrough/parameters.js
@@ -58,6 +58,6 @@ ensureSetParameterFailure(dbConn, "journalCommitInterval", 0);
 ensureSetParameterFailure(dbConn, "syncdelay", 10 * 1000 * 1000);
 ensureSetParameterFailure(dbConn, "syncdelay", -10 * 1000 * 1000);
 
-MongoRunner.stopMongod(dbConn.port);
+MongoRunner.stopMongod(dbConn);
 
 jsTest.log("noPassthrough_parameters_test succeeded!");
diff --git a/jstests/noPassthrough/split_collections_and_indexes.js b/jstests/noPassthrough/split_collections_and_indexes.js
index 3ad5f95d999..9ad12b3eb48 100644
--- a/jstests/noPassthrough/split_collections_and_indexes.js
+++ b/jstests/noPassthrough/split_collections_and_indexes.js
@@ -13,7 +13,7 @@ if (!jsTest.options().storageEngine || jsTest.options().storageEngine === "wired
     assert(listFiles(dbpath + "/index").length > 0);
     assert(listFiles(dbpath + "/collection").length > 0);
 
-    MongoRunner.stopMongod(m.port);
+    MongoRunner.stopMongod(m);
 
     // Subsequent attempts to start server using same dbpath but different
     // wiredTigerDirectoryForIndexes and directoryperdb options should fail.
diff --git a/jstests/noPassthrough/sync_write.js b/jstests/noPassthrough/sync_write.js
index b2f2fa24a45..8908d6bad5e 100644
--- a/jstests/noPassthrough/sync_write.js
+++ b/jstests/noPassthrough/sync_write.js
@@ -20,7 +20,7 @@
     // Now connect to the mongod, do a journaled write and abruptly stop the server.
     var testDB = conn.getDB('test');
     assert.writeOK(testDB.synced.insert({synced: true}, {writeConcern: {j: true}}));
-    MongoRunner.stopMongod(conn, 9);
+    MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     // Restart the mongod.
     conn = MongoRunner.runMongod(mongodArgs);
diff --git a/jstests/noPassthrough/wt_nojournal_fsync.js b/jstests/noPassthrough/wt_nojournal_fsync.js
index e5be8b9659e..3fd7d9ff05a 100644
--- a/jstests/noPassthrough/wt_nojournal_fsync.js
+++ b/jstests/noPassthrough/wt_nojournal_fsync.js
@@ -18,7 +18,7 @@ function writeDataAndRestart(doFsync) {
     }
 
     jsTestLog("kill -9");
-    MongoRunner.stopMongod(conn, /*signal*/ 9);
+    MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     jsTestLog("restart node");
     conn = MongoRunner.runMongod({
diff --git a/jstests/noPassthrough/wt_nojournal_repl.js b/jstests/noPassthrough/wt_nojournal_repl.js
index ebea3f1b5ab..2805d1506cf 100644
--- a/jstests/noPassthrough/wt_nojournal_repl.js
+++ b/jstests/noPassthrough/wt_nojournal_repl.js
@@ -61,7 +61,7 @@ if (jsTest.options().storageEngine && jsTest.options().storageEngine !== "wiredT
     assert.commandWorked(secondary1.getDB("admin").runCommand({fsync: 1}));
 
     jsTestLog("kill -9 secondary 1");
-    MongoRunner.stopMongod(secondary1.port, /*signal*/ 9);
+    MongoRunner.stopMongod(secondary1, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     jsTestLog("add some data to a new collection bar");
     for (var i = 0; i < 100; i++) {
diff --git a/jstests/noPassthrough/wt_nojournal_skip_recovery.js b/jstests/noPassthrough/wt_nojournal_skip_recovery.js
index df3b32609d0..7a5b0e7dc31 100644
--- a/jstests/noPassthrough/wt_nojournal_skip_recovery.js
+++ b/jstests/noPassthrough/wt_nojournal_skip_recovery.js
@@ -51,7 +51,7 @@
         function() {
             var count = conn.getDB('test').nojournal.count({journaled: {$exists: true}});
             if (count >= 100) {
-                MongoRunner.stopMongod(conn, 9);
+                MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
                 return true;
             }
             return false;
diff --git a/jstests/noPassthrough/wt_nojournal_toggle.js b/jstests/noPassthrough/wt_nojournal_toggle.js
index 8973c37b2f5..f09f92f6a95 100644
--- a/jstests/noPassthrough/wt_nojournal_toggle.js
+++ b/jstests/noPassthrough/wt_nojournal_toggle.js
@@ -60,7 +60,7 @@
                 // do an extra journaled write to make all visible commits durable, before killing
                 // the mongod.
                 assert.writeOK(testDB.nojournal.insert({final: true}, {writeConcern: {j: true}}));
-                MongoRunner.stopMongod(conn, 9);
+                MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
                 return true;
             }
             return false;
diff --git a/jstests/noPassthrough/wt_unclean_shutdown.js b/jstests/noPassthrough/wt_unclean_shutdown.js
index 112413ec61b..74dceda2a5c 100644
--- a/jstests/noPassthrough/wt_unclean_shutdown.js
+++ b/jstests/noPassthrough/wt_unclean_shutdown.js
@@ -83,7 +83,7 @@ load('jstests/libs/parallelTester.js');  // For ScopedThread
 
     // Mongod needs an unclean shutdown so that WT recovery is forced on restart and we can detect
     // any missing records.
-    MongoRunner.stopMongod(conn, 9);
+    MongoRunner.stopMongod(conn, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
 
     // Retrieve the start and end data from each thread.
     var retData = [];
diff --git a/jstests/noPassthroughWithMongod/indexbg_restart_secondary.js b/jstests/noPassthroughWithMongod/indexbg_restart_secondary.js
index a84e2b57293..26b8083de75 100644
--- a/jstests/noPassthroughWithMongod/indexbg_restart_secondary.js
+++ b/jstests/noPassthroughWithMongod/indexbg_restart_secondary.js
@@ -27,8 +27,6 @@
     var master = replTest.getPrimary();
     var second = replTest.getSecondary();
 
-    var secondId = replTest.getNodeId(second);
-
     var masterDB = master.getDB('bgIndexSec');
     var secondDB = second.getDB('bgIndexSec');
 
@@ -60,7 +58,9 @@
     // the oplog entry so it isn't replayed. If (A) is present without (B), then there are two ways
     // that the index can be rebuilt on startup and this test is only for the one triggered by (A).
     secondDB.adminCommand({fsync: 1});
-    replTest.restart(secondId, {}, /*signal=*/9, /*wait=*/true);
+
+    MongoRunner.stopMongod(second, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
+    replTest.start(second, {}, /*restart=*/true, /*wait=*/true);
 
     // Make sure secondary comes back.
     assert.soon(function() {
diff --git a/jstests/noPassthroughWithMongod/indexbg_restart_secondary_noretry.js b/jstests/noPassthroughWithMongod/indexbg_restart_secondary_noretry.js
index 747c8b2e6b8..05e1e2bed8f 100644
--- a/jstests/noPassthroughWithMongod/indexbg_restart_secondary_noretry.js
+++ b/jstests/noPassthroughWithMongod/indexbg_restart_secondary_noretry.js
@@ -26,8 +26,6 @@
     var master = replTest.getPrimary();
     var second = replTest.getSecondary();
 
-    var secondId = replTest.getNodeId(second);
-
     var masterDB = master.getDB('bgIndexNoRetrySec');
     var secondDB = second.getDB('bgIndexNoRetrySec');
 
@@ -58,7 +56,8 @@
     // the oplog entry so it isn't replayed. If (A) is present without (B), then there are two ways
     // that the index can be rebuilt on startup and this test is only for the one triggered by (A).
     secondDB.adminCommand({fsync: 1});
-    replTest.restart(secondId, {}, /*signal=*/9, /*wait=*/true);
+    replTest.stop(second, 9, {allowedExitCode: MongoRunner.EXIT_SIGKILL});
+    replTest.start(second, {}, /*restart*/ true, /*wait=*/true);
 
     // Make sure secondary comes back.
     assert.soon(function() {
diff --git a/jstests/noPassthroughWithMongod/logpath.js b/jstests/noPassthroughWithMongod/logpath.js
index 3b6b2069937..eea71efdc4f 100644
--- a/jstests/noPassthroughWithMongod/logpath.js
+++ b/jstests/noPassthroughWithMongod/logpath.js
@@ -57,7 +57,7 @@ var m = MongoRunner.runMongod({port: port[0], dbpath: dbdir, logpath: logdir + l
 
 // log should now exist (and no rotations should exist)
 assert.eq(logCount(logs[0], true), 1);
-MongoRunner.stopMongod(port[0]);
+MongoRunner.stopMongod(m /*port[0]*/);
 
 print("------ Start mongod with logpath set to existing file");
 m = MongoRunner.runMongod({port: port[1], dbpath: dbdir, logpath: logdir + logs[0]});
@@ -69,7 +69,7 @@ assert.eq(logCount(logs[0]), 1);
 assert.eq(logCount(logs[0], true), 2);
 cleanupFiles();
 
-MongoRunner.stopMongod(port[1]);
+MongoRunner.stopMongod(m /*port[1]*/);
 
 // Blocking on SERVER-5117:
 // MongoRunner currently hangs if mongod fails to start so these tests don't work
@@ -85,7 +85,7 @@ if (false) {
 
         // log should now exist (and no rotations should exist)
         assert.eq(logCount(logs[1], true), 1);
-        MongoRunner.stopMongod(port[2]);
+        MongoRunner.stopMongod(m /*port[2]*/);
 
         print("------ Start mongod with logpath set to existing file, fork");
         m = MongoRunner.runMongod(
@@ -98,7 +98,7 @@ if (false) {
         assert.eq(logCount(logs[1], true), 2);
         cleanupFiles();
 
-        MongoRunner.stopMongod(port[3]);
+        MongoRunner.stopMongod(m /*port[3]*/);
     }
 
     // the following tests depend on undefined behavior; assume that MongoRunner raises exception on
diff --git a/jstests/noPassthroughWithMongod/reconfigwt.js b/jstests/noPassthroughWithMongod/reconfigwt.js
index 4176022e971..b7ae40891b2 100644
--- a/jstests/noPassthroughWithMongod/reconfigwt.js
+++ b/jstests/noPassthroughWithMongod/reconfigwt.js
@@ -33,5 +33,5 @@ if (ss.storageEngine.name !== "wiredTiger") {
     assert.commandFailed(reconfigure("eviction_target=a"));
     assert.commandFailed(reconfigure("fake_config_key=1"));
 
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 }
diff --git a/jstests/noPassthroughWithMongod/testing_only_commands.js b/jstests/noPassthroughWithMongod/testing_only_commands.js
index eeacd588974..55187010cc1 100644
--- a/jstests/noPassthroughWithMongod/testing_only_commands.js
+++ b/jstests/noPassthroughWithMongod/testing_only_commands.js
@@ -37,7 +37,7 @@ var conn = MongoRunner.runMongod({});
 for (i in testOnlyCommands) {
     assertCmdNotFound(conn.getDB('test'), testOnlyCommands[i]);
 }
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 // Now enable the commands
 jsTest.setOption('enableTestCommands', true);
@@ -46,4 +46,4 @@ var conn = MongoRunner.runMongod({});
 for (i in testOnlyCommands) {
     assertCmdFound(conn.getDB('test'), testOnlyCommands[i]);
 }
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
diff --git a/jstests/noPassthroughWithMongod/ttl_repl_maintenance.js b/jstests/noPassthroughWithMongod/ttl_repl_maintenance.js
index 45a5d752106..44250c4f1d2 100644
--- a/jstests/noPassthroughWithMongod/ttl_repl_maintenance.js
+++ b/jstests/noPassthroughWithMongod/ttl_repl_maintenance.js
@@ -19,7 +19,7 @@ var primeSystemReplset = function() {
 };
 
 var restartWithConfig = function() {
-    MongoRunner.stopMongod(conn.port, 15);
+    MongoRunner.stopMongod(conn);
     conn = MongoRunner.runMongod({restart: true, cleanData: false, dbpath: conn.dbpath});
     testDB = conn.getDB("test");
     var n = 100;
@@ -37,7 +37,7 @@ var restartWithoutConfig = function() {
     var localDB = conn.getDB("local");
     assert.writeOK(localDB.system.replset.remove({}));
 
-    MongoRunner.stopMongod(conn.port, 15);
+    MongoRunner.stopMongod(conn);
 
     conn = MongoRunner.runMongod({restart: true, cleanData: false, dbpath: conn.dbpath});
 
@@ -45,7 +45,7 @@ var restartWithoutConfig = function() {
         return conn.getDB("test").foo.count() < 100;
     }, "never deleted", 75000);
 
-    MongoRunner.stopMongod(conn.port, 15);
+    MongoRunner.stopMongod(conn);
 };
 
 print("Create a TTL collection and put doc in local.system.replset");
diff --git a/jstests/replsets/auth1.js b/jstests/replsets/auth1.js
index 69bba87a81d..4c4110597c5 100644
--- a/jstests/replsets/auth1.js
+++ b/jstests/replsets/auth1.js
@@ -40,7 +40,6 @@ load("jstests/replsets/rslib.js");
     print("should fail with wrong permissions");
     assert.eq(
         m, _isWindows() ? 100 : 1, "mongod should exit w/ 1 (EXIT_FAILURE): permissions too open");
-    MongoRunner.stopMongod(port[0]);
 
     // Pre-populate the data directory for the first replica set node, to be started later, with
     // a user's credentials.
diff --git a/jstests/replsets/cloneDb.js b/jstests/replsets/cloneDb.js
index a24b9d80c11..5590dd027f1 100644
--- a/jstests/replsets/cloneDb.js
+++ b/jstests/replsets/cloneDb.js
@@ -117,7 +117,7 @@
             'cloneDatabase from standalone to SECONDARY succeeded and should not accept writes');
 
         jsTest.log("Shut down replica set and standalone server");
-        MongoRunner.stopMongod(standalone.port);
+        MongoRunner.stopMongod(standalone);
 
         replTest.stopSet();
     }
diff --git a/jstests/replsets/initial_sync_invalid_index_spec.js b/jstests/replsets/initial_sync_invalid_index_spec.js
index ce608334e8b..fc6e8dd7f77 100644
--- a/jstests/replsets/initial_sync_invalid_index_spec.js
+++ b/jstests/replsets/initial_sync_invalid_index_spec.js
@@ -22,7 +22,7 @@
         {createIndexes: "test", indexes: [{v: 2, name: "x_1", key: {x: 1}, invalidOption: 1}]}));
 
     // Add another node to the replica set to allow an initial sync to occur.
-    replTest.add();
+    var init_sync_node = replTest.add();
 
     clearRawMongoProgramOutput();
     reInitiateWithoutThrowingOnAbortedMember(replTest);
@@ -36,8 +36,7 @@
     };
     assert.soon(assertFn, "Initial sync should have aborted on invalid index specification");
 
-    replTest.stopSet(undefined,
-                     undefined,
-                     {allowedExitCodes: [MongoRunner.EXIT_ABRUPT, MongoRunner.EXIT_ABORT]});
+    replTest.stop(init_sync_node, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+    replTest.stopSet();
 
 })();
diff --git a/jstests/replsets/initial_sync_unsupported_auth_schema.js b/jstests/replsets/initial_sync_unsupported_auth_schema.js
index f097c8469df..8e63c0039c1 100644
--- a/jstests/replsets/initial_sync_unsupported_auth_schema.js
+++ b/jstests/replsets/initial_sync_unsupported_auth_schema.js
@@ -19,7 +19,7 @@ function testInitialSyncAbortsWithUnsupportedAuthSchema(schema) {
     assert.writeOK(res);
 
     // Add another node to the replica set to allow an initial sync to occur
-    rst.add();
+    var init_sync_node = rst.add();
 
     clearRawMongoProgramOutput();
     reInitiateWithoutThrowingOnAbortedMember(rst);
@@ -45,9 +45,8 @@ function testInitialSyncAbortsWithUnsupportedAuthSchema(schema) {
                     ' authSchema version: ' + tojson(schema),
                 60000);
 
-    rst.stopSet(undefined,
-                undefined,
-                {allowedExitCodes: [MongoRunner.EXIT_ABRUPT, MongoRunner.EXIT_ABORT]});
+    rst.stop(init_sync_node, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+    rst.stopSet();
 }
 
 function testInitialSyncAbortsWithExistingUserAndNoAuthSchema() {
@@ -66,7 +65,7 @@ function testInitialSyncAbortsWithExistingUserAndNoAuthSchema() {
     assert.writeOK(res);
 
     // Add another node to the replica set to allow an initial sync to occur
-    rst.add();
+    var init_sync_node = rst.add();
 
     clearRawMongoProgramOutput();
     reInitiateWithoutThrowingOnAbortedMember(rst);
@@ -88,9 +87,8 @@ function testInitialSyncAbortsWithExistingUserAndNoAuthSchema() {
                     ' a missing auth schema',
                 60000);
 
-    rst.stopSet(undefined,
-                undefined,
-                {allowedExitCodes: [MongoRunner.EXIT_ABRUPT, MongoRunner.EXIT_ABORT]});
+    rst.stop(init_sync_node, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+    rst.stopSet();
 }
 
 testInitialSyncAbortsWithUnsupportedAuthSchema({_id: 'authSchema'});
diff --git a/jstests/replsets/invalid_index_spec.js b/jstests/replsets/invalid_index_spec.js
index d227854e6f7..80f5da09055 100644
--- a/jstests/replsets/invalid_index_spec.js
+++ b/jstests/replsets/invalid_index_spec.js
@@ -38,8 +38,6 @@
     };
     assert.soon(assertFn, "Replication should have aborted on invalid index specification", 60000);
 
-    replTest.stopSet(undefined,
-                     undefined,
-                     {allowedExitCodes: [MongoRunner.EXIT_ABRUPT, MongoRunner.EXIT_ABORT]});
-
+    replTest.stop(replTest.getSecondary(), undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+    replTest.stopSet();
 })();
diff --git a/jstests/replsets/oplog_replay_on_startup_with_bad_op.js b/jstests/replsets/oplog_replay_on_startup_with_bad_op.js
index a58d94ec84b..e238cc05955 100644
--- a/jstests/replsets/oplog_replay_on_startup_with_bad_op.js
+++ b/jstests/replsets/oplog_replay_on_startup_with_bad_op.js
@@ -61,5 +61,5 @@
               "If the Timestamps differ, the server may be filling in the null timestamps");
 
     assert.throws(() => rst.restart(0));  // Restart in replSet mode again.
-    print('\n\n\t\t^^^^^^^^  This was supposed to fassert ^^^^^^^^^^^\n\n');
+    rst.stopSet();
 })();
diff --git a/jstests/replsets/rollback_cmd_unrollbackable.js b/jstests/replsets/rollback_cmd_unrollbackable.js
index 0abc3384db6..4d8acdb312a 100644
--- a/jstests/replsets/rollback_cmd_unrollbackable.js
+++ b/jstests/replsets/rollback_cmd_unrollbackable.js
@@ -74,4 +74,5 @@ assert.soon(function() {
     return rawMongoProgramOutput().match(msg);
 }, "Did not see a log entry about skipping the nonrollbackable command during rollback");
 
-replTest.stopSet(undefined, undefined, {allowedExitCodes: [MongoRunner.EXIT_ABRUPT]});
+replTest.stop(BID, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+replTest.stopSet();
diff --git a/jstests/replsets/rollback_collMod_fatal.js b/jstests/replsets/rollback_collMod_fatal.js
index b73b1e53440..c4409ced190 100644
--- a/jstests/replsets/rollback_collMod_fatal.js
+++ b/jstests/replsets/rollback_collMod_fatal.js
@@ -64,4 +64,5 @@ assert.soon(function() {
     return rawMongoProgramOutput().match("cannot rollback a collMod command");
 }, "B failed to fassert");
 
-replTest.stopSet(undefined, undefined, {allowedExitCodes: [MongoRunner.EXIT_ABRUPT]});
+replTest.stop(BID, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+replTest.stopSet();
\ No newline at end of file
diff --git a/jstests/replsets/rollback_dropdb.js b/jstests/replsets/rollback_dropdb.js
index 3944f7b821e..f3ee7607437 100644
--- a/jstests/replsets/rollback_dropdb.js
+++ b/jstests/replsets/rollback_dropdb.js
@@ -64,4 +64,5 @@ assert.soon(function() {
         "rollback : can't rollback drop database full resync will be required");
 }, "B failed to fassert");
 
-replTest.stopSet(undefined, undefined, {allowedExitCodes: [MongoRunner.EXIT_ABRUPT]});
+replTest.stop(BID, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+replTest.stopSet();
\ No newline at end of file
diff --git a/jstests/replsets/rollback_too_new.js b/jstests/replsets/rollback_too_new.js
index 131d80a54fe..75aa8ec0fc4 100644
--- a/jstests/replsets/rollback_too_new.js
+++ b/jstests/replsets/rollback_too_new.js
@@ -66,6 +66,6 @@
         }
     }, "node C failed to fassert", 60 * 1000);
 
-    replTest.stopSet(undefined, undefined, {allowedExitCodes: [MongoRunner.EXIT_ABRUPT]});
-
+    replTest.stop(CID, undefined, {allowedExitCode: MongoRunner.EXIT_ABRUPT});
+    replTest.stopSet();
 }());
diff --git a/jstests/replsets/shutdown.js b/jstests/replsets/shutdown.js
index e16e9af06b3..b35172a808f 100644
--- a/jstests/replsets/shutdown.js
+++ b/jstests/replsets/shutdown.js
@@ -19,10 +19,11 @@ load('jstests/replsets/rslib.js');
     rst.initiate(conf);
     rst.awaitReplication();
 
-    let id = rst.getNodeId(rst.getSecondary());
-    rst.stop(id);
+    let secondary = rst.getSecondary();
+    rst.stop(secondary);
     let program = rst.start(
-        id, {waitForConnect: false, setParameter: "failpoint.shutdownAtStartup={mode:'alwaysOn'}"});
+        secondary,
+        {waitForConnect: false, setParameter: "failpoint.shutdownAtStartup={mode:'alwaysOn'}"});
     // mongod should exit automatically, since failpoint was set.
     let exitCode = waitProgram(program.pid);
     assert.eq(0, exitCode);
diff --git a/jstests/sharding/auth_no_config_primary.js b/jstests/sharding/auth_no_config_primary.js
index 0fdd2f31a89..a767ce4eee7 100644
--- a/jstests/sharding/auth_no_config_primary.js
+++ b/jstests/sharding/auth_no_config_primary.js
@@ -17,7 +17,7 @@
 
     // Kill all secondaries, forcing the current primary to step down.
     st.configRS.getSecondaries().forEach(function(secondaryConn) {
-        MongoRunner.stopMongod(secondaryConn.port);
+        MongoRunner.stopMongod(secondaryConn);
     });
 
     // Test authenticate through a fresh connection.
diff --git a/jstests/sharding/convert_to_and_from_sharded.js b/jstests/sharding/convert_to_and_from_sharded.js
index e838559e0f8..08024a64104 100644
--- a/jstests/sharding/convert_to_and_from_sharded.js
+++ b/jstests/sharding/convert_to_and_from_sharded.js
@@ -88,7 +88,7 @@
         return res.state == 'completed';
     });
 
-    MongoRunner.stopMongod(newMongod.port);
+    MongoRunner.stopMongod(newMongod);
 
     checkBasicCRUD(st.s.getDB('test').unsharded);
     checkBasicCRUD(st.s.getDB('test').sharded);
diff --git a/jstests/sharding/implicit_db_creation.js b/jstests/sharding/implicit_db_creation.js
index ed202ff2ea5..10442f7e97a 100644
--- a/jstests/sharding/implicit_db_creation.js
+++ b/jstests/sharding/implicit_db_creation.js
@@ -40,7 +40,7 @@
 
     assert.neq(null, configDB.databases.findOne({_id: 'unshardedDB'}));
 
-    MongoRunner.stopMongod(newShardConn.port);
+    MongoRunner.stopMongod(newShardConn);
     st.stop();
 
 })();
diff --git a/jstests/sharding/lagged_config_secondary.js b/jstests/sharding/lagged_config_secondary.js
index 0525e24aaae..3d109dd9056 100644
--- a/jstests/sharding/lagged_config_secondary.js
+++ b/jstests/sharding/lagged_config_secondary.js
@@ -26,7 +26,7 @@
     assert.writeOK(st.getDB('config').TestConfigColl.insert({TestKey: 'Test value'}));
 
     st.configRS.stopMaster();
-    MongoRunner.stopMongod(configSecondaryToKill.port);
+    MongoRunner.stopMongod(configSecondaryToKill);
 
     // Clears all cached info so mongos will be forced to query from the config.
     st.s.adminCommand({flushRouterConfig: 1});
diff --git a/jstests/sharding/localhostAuthBypass.js b/jstests/sharding/localhostAuthBypass.js
index cd152410e3c..319c0eb2b79 100644
--- a/jstests/sharding/localhostAuthBypass.js
+++ b/jstests/sharding/localhostAuthBypass.js
@@ -35,7 +35,7 @@
         } else {
             assert.commandFailed(res, "Add shard");
         }
-        return m.port;
+        return m;
     };
 
     var findEmptyShard = function(st, ns) {
@@ -201,22 +201,22 @@
         // information.  Therefore, we'll do this manually for now.
 
         for (var i = 0; i < st._mongos.length; i++) {
-            var port = st["s" + i].port;
-            MongoRunner.stopMongos(port,
+            var conn = st["s" + i];
+            MongoRunner.stopMongos(conn,
                                    /*signal*/ false,
                                    {auth: {user: username, pwd: password}});
         }
 
         for (var i = 0; i < st._connections.length; i++) {
-            var port = st["shard" + i].port;
-            MongoRunner.stopMongod(port,
+            var conn = st["shard" + i];
+            MongoRunner.stopMongod(conn,
                                    /*signal*/ false,
                                    {auth: {user: username, pwd: password}});
         }
 
         for (var i = 0; i < st._configServers.length; i++) {
-            var c = st["config" + i].port;
-            MongoRunner.stopMongod(port,
+            var conn = st["config" + i];
+            MongoRunner.stopMongod(conn,
                                    /*signal*/ false,
                                    {auth: {user: username, pwd: password}});
         }
diff --git a/jstests/sharding/shard_aware_init.js b/jstests/sharding/shard_aware_init.js
index d6e27c7297c..386755dd9b2 100644
--- a/jstests/sharding/shard_aware_init.js
+++ b/jstests/sharding/shard_aware_init.js
@@ -37,14 +37,14 @@
         var restartAndFixShardIdentityDoc = function(startOptions) {
             var options = Object.extend({}, startOptions);
             delete options.shardsvr;
-            mongodConn = MongoRunner.runMongod(options);
+            var mongodConn = MongoRunner.runMongod(options);
             waitForMaster(mongodConn);
 
             var res = mongodConn.getDB('admin').system.version.update({_id: 'shardIdentity'},
                                                                       shardIdentityDoc);
             assert.eq(1, res.nModified);
 
-            MongoRunner.stopMongod(mongodConn.port);
+            MongoRunner.stopMongod(mongodConn);
 
             newMongodOptions.shardsvr = '';
             mongodConn = MongoRunner.runMongod(newMongodOptions);
@@ -87,8 +87,7 @@
         //
 
         var newMongodOptions = Object.extend(mongodConn.savedOptions, {restart: true});
-
-        MongoRunner.stopMongod(mongodConn.port);
+        MongoRunner.stopMongod(mongodConn);
         mongodConn = MongoRunner.runMongod(newMongodOptions);
         waitForMaster(mongodConn);
 
@@ -104,7 +103,7 @@
         //
 
         // Note: modification of the shardIdentity is allowed only when not running with --shardsvr
-        MongoRunner.stopMongod(mongodConn.port);
+        MongoRunner.stopMongod(mongodConn);
         delete newMongodOptions.shardsvr;
         mongodConn = MongoRunner.runMongod(newMongodOptions);
         waitForMaster(mongodConn);
@@ -112,7 +111,7 @@
         assert.writeOK(mongodConn.getDB('admin').system.version.update(
             {_id: 'shardIdentity'}, {_id: 'shardIdentity', shardName: 'x', clusterId: ObjectId()}));
 
-        MongoRunner.stopMongod(mongodConn.port);
+        MongoRunner.stopMongod(mongodConn);
 
         newMongodOptions.shardsvr = '';
         assert.throws(function() {
@@ -124,14 +123,10 @@
         // Test that it is possible to fix the invalid shardIdentity doc by not passing --shardsvr
         //
 
-        try {
-            // The server was terminated not by calling stopMongod earlier, this will cleanup
-            // the process from registry in shell_utils_launcher.
-            MongoRunner.stopMongod(newMongodOptions.port);
-        } catch (ex) {
-            if (!(ex instanceof (MongoRunner.StopError))) {
-                throw ex;
-            }
+        // If mongodConn is not null, the server terminated after MongoRunner.runMongod() had
+        // returned. So we call stopMongod again to clean up the registry in shell_util_launcher.cpp
+        if (mongodConn) {
+            MongoRunner.stopMongod(mongodConn);
         }
 
         mongodConn = restartAndFixShardIdentityDoc(newMongodOptions);
@@ -145,7 +140,7 @@
 
     runTest(mongod, st.configRS.getURL());
 
-    MongoRunner.stopMongod(mongod.port);
+    MongoRunner.stopMongod(mongod);
 
     var replTest = new ReplSetTest({nodes: 1});
     replTest.startSet({shardsvr: ''});
diff --git a/jstests/sharding/shard_aware_on_add_shard.js b/jstests/sharding/shard_aware_on_add_shard.js
index 11c08349b60..92c490f2982 100644
--- a/jstests/sharding/shard_aware_on_add_shard.js
+++ b/jstests/sharding/shard_aware_on_add_shard.js
@@ -44,7 +44,7 @@
     checkShardingStateInitialized(standaloneConn, st.configRS.getURL(), newShardName, clusterId);
     checkShardMarkedAsShardAware(st.s, newShardName);
 
-    MongoRunner.stopMongod(standaloneConn.port);
+    MongoRunner.stopMongod(standaloneConn);
 
     // Add a shard that is a replica set.
 
diff --git a/jstests/sharding/shard_identity_config_update.js b/jstests/sharding/shard_identity_config_update.js
index 6d3b01deb41..dccdd03c669 100644
--- a/jstests/sharding/shard_identity_config_update.js
+++ b/jstests/sharding/shard_identity_config_update.js
@@ -73,7 +73,7 @@
     st.rs0.stop(0);
     st.rs0.stop(1);
 
-    MongoRunner.stopMongod(newNode.port);
+    MongoRunner.stopMongod(newNode);
 
     replConfig = st.configRS.getReplSetConfigFromNode();
     replConfig.version += 1;
diff --git a/jstests/sharding/shard_kill_and_pooling.js b/jstests/sharding/shard_kill_and_pooling.js
index 369ebe6c3ee..54c5e9306bf 100644
--- a/jstests/sharding/shard_kill_and_pooling.js
+++ b/jstests/sharding/shard_kill_and_pooling.js
@@ -57,7 +57,9 @@ for (var test = 0; test < 2; test++) {
         // Flush writes to disk, since sometimes we're killing uncleanly
         assert(mongos.getDB("admin").runCommand({fsync: 1}).ok);
 
-        MongoRunner.stopMongod(st.shard0, killWith);
+        var exitCode = killWith === 9 ? MongoRunner.EXIT_SIGKILL : MongoRunner.EXIT_CLEAN;
+
+        MongoRunner.stopMongod(st.shard0, killWith, {allowedExitCode: exitCode});
 
         jsTest.log("Restart shard...");
 
diff --git a/jstests/ssl/libs/ssl_helpers.js b/jstests/ssl/libs/ssl_helpers.js
index 50463d8dec9..225b98a60ce 100644
--- a/jstests/ssl/libs/ssl_helpers.js
+++ b/jstests/ssl/libs/ssl_helpers.js
@@ -50,7 +50,7 @@ var replShouldFail = function(name, opt1, opt2) {
     assert.throws(load, [replSetTestFile], "This setup should have failed");
     // clean up to continue running...
     if (replTest) {
-        replTest.stopSet(15);
+        replTest.stopSet();
     }
 };
 
diff --git a/jstests/ssl/set_parameter_ssl.js b/jstests/ssl/set_parameter_ssl.js
index 407ed8b0834..a07db207b79 100644
--- a/jstests/ssl/set_parameter_ssl.js
+++ b/jstests/ssl/set_parameter_ssl.js
@@ -13,7 +13,7 @@ function testSSLTransition(oldMode, newMode, shouldSucceed) {
     var res = adminDB.runCommand({"setParameter": 1, "sslMode": newMode});
 
     assert(res["ok"] == shouldSucceed, tojson(res));
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 }
 
 function testAuthModeTransition(oldMode, newMode, sslMode, shouldSucceed) {
@@ -30,7 +30,7 @@ function testAuthModeTransition(oldMode, newMode, sslMode, shouldSucceed) {
     var res = adminDB.runCommand({"setParameter": 1, "clusterAuthMode": newMode});
 
     assert(res["ok"] == shouldSucceed, tojson(res));
-    MongoRunner.stopMongod(conn.port);
+    MongoRunner.stopMongod(conn);
 }
 
 testSSLTransition("allowSSL", "invalid", false);
diff --git a/jstests/ssl/ssl_cert_password.js b/jstests/ssl/ssl_cert_password.js
index 064669ba2c6..a9590d92777 100644
--- a/jstests/ssl/ssl_cert_password.js
+++ b/jstests/ssl/ssl_cert_password.js
@@ -168,6 +168,6 @@ assert.eq(md5, md5_stored, "hash of stored file does not match the expected valu
 
 if (!_isWindows()) {
     // Stop the server
-    var exitCode = MongoRunner.stopMongod(md.port, 15);
+    var exitCode = MongoRunner.stopMongod(md);
     assert(exitCode == 0);
 }
diff --git a/jstests/ssl/ssl_hostname_validation.js b/jstests/ssl/ssl_hostname_validation.js
index 9801e14807c..d61109293ba 100644
--- a/jstests/ssl/ssl_hostname_validation.js
+++ b/jstests/ssl/ssl_hostname_validation.js
@@ -58,7 +58,7 @@ function testCombination(certPath, allowInvalidHost, allowInvalidCert, shouldSuc
         assert.eq(
             1, mongo, "Connection attempt succeeded when it should fail certPath: " + certPath);
     }
-    MongoRunner.stopMongod(mongod.port);
+    MongoRunner.stopMongod(mongod);
 }
 
 // 1. Test client connections with different server certificates
diff --git a/jstests/ssl/ssl_options.js b/jstests/ssl/ssl_options.js
index 571f854851b..d1c0c04adcd 100644
--- a/jstests/ssl/ssl_options.js
+++ b/jstests/ssl/ssl_options.js
@@ -36,6 +36,6 @@ assert.eq(getCmdLineOptsResult.parsed.net.ssl.clusterPassword,
           "<password>",
           "Password not properly censored: " + tojson(getCmdLineOptsResult));
 
-MongoRunner.stopMongod(mongodSource.port);
+MongoRunner.stopMongod(mongodSource);
 
 print(baseName + " succeeded.");
diff --git a/jstests/ssl/ssl_with_system_ca.js b/jstests/ssl/ssl_with_system_ca.js
index 3d96651ff94..194712c98ca 100644
--- a/jstests/ssl/ssl_with_system_ca.js
+++ b/jstests/ssl/ssl_with_system_ca.js
@@ -31,7 +31,7 @@
         var exitStatus = runMongoProgram.apply(null, argv);
         assert.eq(exitStatus, 0, "successfully connected with SSL");
 
-        MongoRunner.stopMongod(conn.port);
+        MongoRunner.stopMongod(conn);
     };
 
     assert.throws(function() {
diff --git a/jstests/ssl/ssl_without_ca.js b/jstests/ssl/ssl_without_ca.js
index 2c7aba380bd..cbc3aaa37f1 100644
--- a/jstests/ssl/ssl_without_ca.js
+++ b/jstests/ssl/ssl_without_ca.js
@@ -32,7 +32,7 @@ var exitStatus = runMongoProgram('mongo',
 
 assert.eq(exitStatus, 0, "authentication via MONGODB-X509 without CA succeeded");
 
-MongoRunner.stopMongod(conn.port);
+MongoRunner.stopMongod(conn);
 
 jsTest.log("Assert mongod doesn\'t start with CA file missing and clusterAuthMode=x509.");
 
diff --git a/jstests/ssl/x509_client.js b/jstests/ssl/x509_client.js
index 5842438b98a..ec9b63e6dba 100644
--- a/jstests/ssl/x509_client.js
+++ b/jstests/ssl/x509_client.js
@@ -88,7 +88,7 @@ var x509_options = {sslMode: "requireSSL", sslPEMKeyFile: SERVER_CERT, sslCAFile
 var mongo = MongoRunner.runMongod(Object.merge(x509_options, {auth: ""}));
 
 authAndTest(mongo);
-MongoRunner.stopMongod(mongo.port);
+MongoRunner.stopMongod(mongo);
 
 print("2. Testing x.509 auth to mongos");
 
diff --git a/jstests/sslSpecial/set_parameter_nossl.js b/jstests/sslSpecial/set_parameter_nossl.js
index 74bab379aa0..95b66bc274f 100644
--- a/jstests/sslSpecial/set_parameter_nossl.js
+++ b/jstests/sslSpecial/set_parameter_nossl.js
@@ -7,12 +7,14 @@ function testTransition(newSSLMode, newClusterAuthMode) {
     // If no parameters are given sslMode defaults to disabled
     var conn = MongoRunner.runMongod({clusterAuthMode: "keyFile"});
     var adminDB = conn.getDB("admin");
+    adminDB.createUser({user: "root", pwd: "pwd", roles: ["root"]});
+    adminDB.auth("root", "pwd");
     var res = adminDB.runCommand({"setParameter": 1, "sslMode": newSSLMode});
-    assert(!res["ok"]);
+    assert.commandFailedWithCode(res, ErrorCodes.BadValue);
 
     var res = adminDB.runCommand({"setParameter": 1, "clusterAuthMode": newClusterAuthMode});
-    assert(!res["ok"]);
-    MongoRunner.stopMongod(conn.port);
+    assert.commandFailedWithCode(res, ErrorCodes.BadValue);
+    MongoRunner.stopMongod(conn);
 }
 
 testTransition("allowSSL", "sendKeyFile");
diff --git a/jstests/tool/dumprestore_excludecollections.js b/jstests/tool/dumprestore_excludecollections.js
index c3f18065ce3..cfda283b46a 100644
--- a/jstests/tool/dumprestore_excludecollections.js
+++ b/jstests/tool/dumprestore_excludecollections.js
@@ -114,7 +114,7 @@ destDB.dropDatabase();
 // times, but that is not tested here because right now MongoRunners can only be configured using
 // javascript objects which do not allow duplicate keys.  See SERVER-14220.
 
-MongoRunner.stopMongod(mongodDest.port);
-MongoRunner.stopMongod(mongodSource.port);
+MongoRunner.stopMongod(mongodDest);
+MongoRunner.stopMongod(mongodSource);
 
 print(testBaseName + " success!");
diff --git a/src/mongo/shell/bridge.js b/src/mongo/shell/bridge.js
index 74e6e674d71..702d823bf97 100644
--- a/src/mongo/shell/bridge.js
+++ b/src/mongo/shell/bridge.js
@@ -81,7 +81,7 @@ function MongoBridge(options) {
     this.connectToBridge = function connectToBridge() {
         var failedToStart = false;
         assert.soon(() => {
-            if (!checkProgram(pid)) {
+            if (!checkProgram(pid).alive) {
                 failedToStart = true;
                 return true;
             }
diff --git a/src/mongo/shell/replsettest.js b/src/mongo/shell/replsettest.js
index 8ad663b0074..dbad80e7036 100644
--- a/src/mongo/shell/replsettest.js
+++ b/src/mongo/shell/replsettest.js
@@ -1715,11 +1715,11 @@ var ReplSetTest = function(opts) {
 
         n = this.getNodeId(n);
 
-        var port = _useBridge ? _unbridgedPorts[n] : this.ports[n];
-        print('ReplSetTest stop *** Shutting down mongod in port ' + port + ' ***');
-        var ret = MongoRunner.stopMongod(port, signal, opts);
+        var conn = _useBridge ? _unbridgedNodes[n] : this.nodes[n];
+        print('ReplSetTest stop *** Shutting down mongod in port ' + conn.port + ' ***');
+        var ret = MongoRunner.stopMongod(conn, signal, opts);
 
-        print('ReplSetTest stop *** Mongod in port ' + port + ' shutdown with code (' + ret +
+        print('ReplSetTest stop *** Mongod in port ' + conn.port + ' shutdown with code (' + ret +
               ') ***');
 
         if (_useBridge) {
diff --git a/src/mongo/shell/servers.js b/src/mongo/shell/servers.js
index a0f58c5b415..69fecc2aab5 100644
--- a/src/mongo/shell/servers.js
+++ b/src/mongo/shell/servers.js
@@ -6,6 +6,11 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
 
     var shellVersion = version;
 
+    // Record the exit codes of mongod and mongos processes that crashed during startup keyed by
+    // pid. This map is cleared when MongoRunner._startWithArgs and MongoRunner.stopMongod/s are
+    // called.
+    var serverExitCodeMap = {};
+
     var _parsePath = function() {
         var dbpath = "";
         for (var i = 0; i < arguments.length; ++i)
@@ -788,10 +793,10 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
         return mongos;
     };
 
-    MongoRunner.StopError = function(message, returnCode) {
+    MongoRunner.StopError = function(returnCode) {
         this.name = "StopError";
-        this.returnCode = returnCode || "non-zero";
-        this.message = message || "MongoDB process stopped with exit code: " + this.returnCode;
+        this.returnCode = returnCode;
+        this.message = "MongoDB process stopped with exit code: " + this.returnCode;
         this.stack = this.toString() + "\n" + (new Error()).stack;
     };
 
@@ -805,6 +810,9 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
     MongoRunner.EXIT_REPLICATION_ERROR = 3;
     MongoRunner.EXIT_NEED_UPGRADE = 4;
     MongoRunner.EXIT_SHARDING_ERROR = 5;
+    // SIGKILL is translated to TerminateProcess() on Windows, which causes the program to
+    // terminate with exit code 1.
+    MongoRunner.EXIT_SIGKILL = _isWindows() ? 1 : -9;
     MongoRunner.EXIT_KILL = 12;
     MongoRunner.EXIT_ABRUPT = 14;
     MongoRunner.EXIT_NTSERVICE_ERROR = 20;
@@ -822,7 +830,7 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
     /**
      * Kills a mongod process.
      *
-     * @param {number} port the port of the process to kill
+     * @param {Mongo} conn the connection object to the process to kill
      * @param {number} signal The signal number to use for killing
      * @param {Object} opts Additional options. Format:
      *    {
@@ -835,44 +843,38 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
      * Note: The auth option is required in a authenticated mongod running in Windows since
      *  it uses the shutdown command, which requires admin credentials.
      */
-    MongoRunner.stopMongod = function(port, signal, opts) {
-
-        if (!port) {
-            print("Cannot stop mongo process " + port);
-            return null;
+    MongoRunner.stopMongod = function(conn, signal, opts) {
+        if (!conn.pid) {
+            throw new Error("first arg must have a `pid` property; " +
+                            "it is usually the object returned from MongoRunner.runMongod/s");
         }
 
         signal = parseInt(signal) || 15;
         opts = opts || {};
 
-        var allowedExitCodes = [MongoRunner.EXIT_CLEAN];
-
-        if (_isWindows()) {
-            // Return code of processes killed with TerminateProcess on Windows
-            allowedExitCodes.push(1);
-        } else {
-            // Return code of processes killed with SIGKILL on POSIX systems
-            allowedExitCodes.push(-9);
-        }
+        var allowedExitCode = MongoRunner.EXIT_CLEAN;
 
-        if (opts.allowedExitCodes) {
-            allowedExitCodes = allowedExitCodes.concat(opts.allowedExitCodes);
+        if (opts.allowedExitCode) {
+            allowedExitCode = opts.allowedExitCode;
         }
 
-        if (port.port)
-            port = parseInt(port.port);
+        var port = parseInt(conn.port);
 
-        if (port instanceof ObjectId) {
-            var opts = MongoRunner.savedOptions(port);
-            if (opts)
-                port = parseInt(opts.port);
+        var pid = conn.pid;
+        // If the return code is in the serverExitCodeMap, it means the server crashed on startup.
+        // We just use the recorded return code instead of stopping the program.
+        var returnCode;
+        if (pid in serverExitCodeMap) {
+            returnCode = serverExitCodeMap[pid];
+            delete serverExitCodeMap[pid];
+        } else {
+            returnCode = _stopMongoProgram(port, signal, opts);
         }
-
-        var returnCode = _stopMongoProgram(parseInt(port), signal, opts);
-
-        if (!Array.contains(allowedExitCodes, returnCode)) {
-            throw new MongoRunner.StopError(
-                `MongoDB process on port ${port} exited with error code ${returnCode}`, returnCode);
+        if (allowedExitCode !== returnCode) {
+            throw new MongoRunner.StopError(returnCode);
+        } else if (returnCode !== MongoRunner.EXIT_CLEAN) {
+            print("MongoDB process on port " + port + " intentionally exited with error code ",
+                  returnCode);
         }
 
         return returnCode;
@@ -1130,6 +1132,7 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
             pid = _startMongoProgram({args: argArray, env: env});
         }
 
+        delete serverExitCodeMap[pid];
         if (!waitForConnect) {
             return {
                 pid: pid,
@@ -1143,10 +1146,10 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
                 conn.pid = pid;
                 return true;
             } catch (e) {
-                if (!checkProgram(pid)) {
+                var res = checkProgram(pid);
+                if (!res.alive) {
                     print("Could not start mongo program at " + port + ", process ended");
-
-                    // Break out
+                    serverExitCodeMap[pid] = res.exitCode;
                     return true;
                 }
             }
@@ -1178,9 +1181,10 @@ var MongoRunner, _startMongod, startMongoProgram, runMongoProgram, startMongoPro
         assert.soon(function() {
             try {
                 m = new Mongo("127.0.0.1:" + port);
+                m.pid = pid;
                 return true;
             } catch (e) {
-                if (!checkProgram(pid)) {
+                if (!checkProgram(pid).alive) {
                     print("Could not start mongo program at " + port + ", process ended");
 
                     // Break out
diff --git a/src/mongo/shell/shell_utils_launcher.cpp b/src/mongo/shell/shell_utils_launcher.cpp
index 8c1efb65a2d..b5c55090ee4 100644
--- a/src/mongo/shell/shell_utils_launcher.cpp
+++ b/src/mongo/shell/shell_utils_launcher.cpp
@@ -745,8 +745,12 @@ BSONObj ClearRawMongoProgramOutput(const BSONObj& args, void* data) {
 
 BSONObj CheckProgram(const BSONObj& args, void* data) {
     ProcessId pid = ProcessId::fromNative(singleArg(args).numberInt());
-    bool isDead = wait_for_pid(pid, false);
-    return BSON(string("") << (!isDead));
+    int exit_code = -123456;  // sentinel value
+    bool isDead = wait_for_pid(pid, false, &exit_code);
+    if (!isDead) {
+        return BSON("" << BSON("alive" << true));
+    }
+    return BSON("" << BSON("alive" << false << "exitCode" << exit_code));
 }
 
 BSONObj WaitProgram(const BSONObj& a, void* data) {
@@ -1002,8 +1006,8 @@ BSONObj getStopMongodOpts(const BSONObj& a) {
 /** stopMongoProgram(port[, signal]) */
 BSONObj StopMongoProgram(const BSONObj& a, void* data) {
     int nFields = a.nFields();
-    verify(nFields >= 1 && nFields <= 3);
-    uassert(15853, "stopMongo needs a number", a.firstElement().isNumber());
+    uassert(ErrorCodes::FailedToParse, "wrong number of arguments", nFields >= 1 && nFields <= 3);
+    uassert(ErrorCodes::BadValue, "stopMongoProgram needs a number", a.firstElement().isNumber());
     int port = int(a.firstElement().number());
     int code = killDb(port, ProcessId::fromNative(0), getSignal(a), getStopMongodOpts(a));
     log() << "shell: stopped mongo program on port " << port;
@@ -1011,11 +1015,13 @@ BSONObj StopMongoProgram(const BSONObj& a, void* data) {
 }
 
 BSONObj StopMongoProgramByPid(const BSONObj& a, void* data) {
-    verify(a.nFields() == 1 || a.nFields() == 2);
-    uassert(15852, "stopMongoByPid needs a number", a.firstElement().isNumber());
+    int nFields = a.nFields();
+    uassert(ErrorCodes::FailedToParse, "wrong number of arguments", nFields >= 1 && nFields <= 3);
+    uassert(
+        ErrorCodes::BadValue, "stopMongoProgramByPid needs a number", a.firstElement().isNumber());
     ProcessId pid = ProcessId::fromNative(int(a.firstElement().number()));
-    int code = killDb(0, pid, getSignal(a));
-    log() << "shell: stopped mongo program on pid " << pid;
+    int code = killDb(0, pid, getSignal(a), getStopMongodOpts(a));
+    log() << "shell: stopped mongo program with pid " << pid;
     return BSON("" << (double)code);
 }