mysql_install_db equivalent for MongoDB? Error 'handle-open: open: Too many open files'

A developer created millions of collections and indexes, this means millions of collection-* and index-* files. I have no administrative login (DB user) on this replicaset (3 node) with mongod 3.2.6. I wish to initialize MongoDB data directory only with Linux commands. In MariaDB there is mysql_install_db command. error message 2017-01-14T05:25:38.674+0000 E STORAGE [thread2] WiredTiger (24) [1484371538:674300][60390:0x7fcc4bc69700], file:WiredTiger.wt, WT_SESSION.checkpoint: /var/vcap/store/mongodb-data/example/WiredTiger.turtle: handle-open: open: Too many open files 2017-01-14T05:25:38.737+0000 I - [conn2] Assertion: 13538:couldn't open [/proc/60390/stat] errno:24 Too many open files 2017-01-14T05:25:38.738+0000 I NETWORK [conn2] end connection 127.0.0.1:39289 (12 connections now open) 2017-01-14T05:25:38.738+0000 I NETWORK [conn6] end connection 127.0.0.1:39347 (12 connections now open) 2017-01-14T05:25:38.738+0000 I NETWORK [conn9] end connection 127.0.0.1:39453 (12 connections now open) 2017-01-14T05:25:38.769+0000 I COMMAND [conn10] command example command: collStats { collstats: "090f42d6-5368-46c6-80 ca-2a8e7e380693" } keyUpdates:0 writeConflicts:0 numYields:0 reslen:9450 locks:{ Global: { acquireCount: { r: 2 } }, Database: { acquireCount: { r: 1 } }, Collection: { acquireCount: { r: 1 } } } protocol:op_query 161ms 2017-01-14T05:25:38.783+0000 E STORAGE [thread2] WiredTiger (24) [1484371538:783882][60390:0x7fcc4bc69700], checkpoint-server: checkpoint server error: Too many open files 2017-01-14T05:25:38.783+0000 E STORAGE [thread2] WiredTiger (-31804) [1484371538:783983][60390:0x7fcc4bc69700], checkpoint-server: the process must exit and restart: WT_PANIC: WiredTiger library panic 2017-01-14T05:25:38.784+0000 I - [thread2] Fatal Assertion 28558 2017-01-14T05:25:38.784+0000 I - [thread2] ***aborting after fassert() failure 2017-01-14T05:25:38.784+0000 I - [WTJournalFlusher] Fatal Assertion 28559 2017-01-14T05:25:38.784+0000 I - [WTJournalFlusher] ***aborting after fassert() failure 2017-01-14T05:25:38.789+0000 F - [thread2] Got signal: 6 (Aborted). 0x1383b32 0x1382c89 0x1383492 0x7fcc50af2330 0x7fcc50753c37 0x7fcc50757028 0x130dba2 0x1109083 0x1ae49dc 0x1ae4e9d 0x1ae5284 0x1a69dbb 0x7fcc50aea184 0x7fcc5081737d ----- BEGIN BACKTRACE ----- {"backtrace":[{"b":"400000","o":"F83B32","s":"_ZN5mongo15printStackTraceERSo"},{"b":"400000","o":"F82C89"},{"b":"400000","o":"F83492"},{"b":"7FCC50AE2000","o":"10330"},{"b":"7FCC5071D000","o":"36C37","s":"gsignal"},{"b":"7FCC5071D000","o":"3A028","s":"abort"},{"b":"400000","o":"F0DBA2","s":"_ZN5mongo13fassertFailedEi"},{"b":"400000","o":"D09083"},{"b":"400000","o":"16E49DC" ,"s":"__wt_eventv"},{"b":"400000","o":"16E4E9D","s":"__wt_err"},{"b":"400000","o":"16E5284","s":"__wt_panic"},{"b":"400000","o":"1669DBB"},{"b":"7FCC50AE2000","o":"8184"},{"b":"7FCC5071D00 0","o":"FA37D","s":"clone"}],"processInfo":{ "mongodbVersion" : "3.2.6", "gitVersion" : "05552b562c7a0b3143a729aaa0838e558dc49b25", "compiledModules" : [ "enterprise" ], "uname" : { "sysna me" : "Linux", "release" : "3.19.0-64-generic", "version" : "#72~14.04.1-Ubuntu SMP Fri Jun 24 17:59:48 UTC 2016", "machine" : "x86_64" }, "somap" : [ { "elfType" : 2, "b" : "400000", "bui ldId" : "88B6197786F38A44F8D924B095DAD84A9E55F2C8" }, { "b" : "7FFF49FFB000", "elfType" : 3, "buildId" : "C89BD46B7CFC47F3E55EF539B3FAF8E450562F6A" }, { "b" : "7FCC52C73000", "path" : "/us r/lib/x86_64-linux-gnu/libsasl2.so.2", "elfType" : 3, "buildId" : "666B276BD134B0E9579B67D4EE333F2D0FB813CD" }, { "b" : "7FCC52806000", "path" : "/usr/lib/x86_64-linux-gnu/libnetsnmpmibs.s o.30", "elfType" : 3, "buildId" : "4630C89B4E7BCCAD8B1B4FFB508962666D6663C2" }, { "b" : "7FCC525F7000", "path" : "/usr/lib/x86_64-linux-gnu/libsensors.so.4", "elfType" : 3, "buildId" : "85 9FDBFDD82F0EFDEB44A433D9D8020A232A35E2" }, { "b" : "7FCC523F3000", "path" : "/lib/x86_64-linux-gnu/libdl.so.2", "elfType" : 3, "buildId" : "DA9B8C234D0FE9FD8CAAC8970A7EC1B6C8F6623F" }, { " b" : "7FCC5218A000", "path" : "/usr/lib/x86_64-linux-gnu/libnetsnmpagent.so.30", "elfType" : 3, "buildId" : "9E02A41B22FEB1F704B60BA109EC5785131A5090" }, { "b" : "7FCC51F80000", "path" : " /lib/x86_64-linux-gnu/libwrap.so.0", "elfType" : 3, "buildId" : 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