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mono crashes during execution of of MaxQuant
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$ uname -rm | |
4.18.5-arch1-1-ARCH x86_64 | |
$ mono --version | |
Mono JIT compiler version 5.21.0 (master/05bc22015c9 Thu Oct 25 13:31:44 CEST 2018) | |
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com | |
TLS: __thread | |
SIGSEGV: altstack | |
Notifications: epoll | |
Architecture: amd64 | |
Disabled: none | |
Misc: softdebug | |
Interpreter: yes | |
LLVM: supported, not enabled. | |
Suspend: hybrid | |
GC: sgen (concurrent by default) | |
$ maxquant --version | |
MaxQuantCmd 1.6.0.16 | |
$ maxquant [...] | |
[...] | |
Apply FDR (SP) | |
couldn't allocate guard page, continue without it | |
couldn't allocate guard page, continue without it | |
* Assertion at mini-exceptions.c:2953, condition `tls->signal_stack' not met | |
Stacktrace: | |
/proc/self/maps: | |
41aa8000-41be8000 rwxp 00000000 00:00 0 | |
41fe7000-41ff7000 rwxp 00000000 00:00 0 | |
56353d8d8000-56353d903000 r--p 00000000 00:17 391951 /usr/bin/mono-sgen | |
56353d903000-56353dc72000 r-xp 0002b000 00:17 391951 /usr/bin/mono-sgen | |
56353dc72000-56353dda5000 r--p 0039a000 00:17 391951 /usr/bin/mono-sgen | |
56353dda6000-56353ddad000 r--p 004cd000 00:17 391951 /usr/bin/mono-sgen | |
56353ddad000-56353ddb2000 rw-p 004d4000 00:17 391951 /usr/bin/mono-sgen | |
56353ddb2000-56353de43000 rw-p 00000000 00:00 0 | |
56353f85f000-563540165000 rw-p 00000000 00:00 0 [heap] | |
7f227cd04000-7f227cd20000 rw-p 00000000 00:00 0 | |
7f227cd28000-7f227cd38000 rw-p 00000000 00:00 0 | |
7f227cd40000-7f227cd44000 rw-p 00000000 00:00 0 | |
7f227cd54000-7f227cd5c000 rw-p 00000000 00:00 0 | |
7f227cd78000-7f227cda0000 rw-p 00000000 00:00 0 | |
7f227cda8000-7f227cdac000 rw-p 00000000 00:00 0 | |
7f227cdb4000-7f227cdbc000 rw-p 00000000 00:00 0 | |
7f227cddc000-7f227cde0000 rw-p 00000000 00:00 0 | |
7f227cde4000-7f227cdec000 rw-p 00000000 00:00 0 | |
7f227cdf4000-7f227ce00000 rw-p 00000000 00:00 0 | |
7f227ce08000-7f227ce10000 rw-p 00000000 00:00 0 | |
7f227ce18000-7f227ce24000 rw-p 00000000 00:00 0 | |
7f227ce2c000-7f227ce30000 rw-p 00000000 00:00 0 | |
7f227ce40000-7f227ce44000 rw-p 00000000 00:00 0 | |
7f227ce4c000-7f227ce50000 rw-p 00000000 00:00 0 | |
7f227ce60000-7f227ce64000 rw-p 00000000 00:00 0 | |
Memory around native instruction pointer (0x7f268d36cd7f): | |
0x7f268d36cd6f d2 4c 89 ce bf 02 00 00 00 b8 0e 00 00 00 0f 05 .L.............. | |
0x7f268d36cd7f 48 8b 8c 24 08 01 00 00 64 48 33 0c 25 28 00 00 H..$....dH3.%(.. | |
0x7f268d36cd8f 00 44 89 c0 75 19 48 81 c4 10 01 00 00 5b c3 66 .D..u.H......[.f | |
0x7f268d36cd9f 90 48 8b 15 99 60 18 00 f7 d8 64 89 02 eb ba 67 .H...`....d....g | |
Native stacktrace: | |
/usr/bin/mono(+0x13addf) [0x56353da12ddf] | |
/usr/bin/mono(+0x13b119) [0x56353da13119] | |
/usr/bin/mono(+0xcacbc) [0x56353d9a2cbc] | |
/usr/lib/libpthread.so.0(+0x123c0) [0x7f268d5253c0] | |
/usr/lib/libc.so.6(gsignal+0x10f) [0x7f268d36cd7f] | |
/usr/lib/libc.so.6(abort+0x125) [0x7f268d357672] | |
/usr/bin/mono(+0x2beb9) [0x56353d903eb9] | |
/usr/bin/mono(monoeg_assertion_message+0xda) [0x56353dc66e1a] | |
/usr/bin/mono(+0xca860) [0x56353d9a2860] | |
/usr/bin/mono(+0x31549) [0x56353d909549] | |
/usr/bin/mono(+0x291b60) [0x56353db69b60] | |
/usr/lib/libpthread.so.0(+0x7a9d) [0x7f268d51aa9d] | |
/usr/lib/libc.so.6(clone+0x43) [0x7f268d430a43] | |
Pkilling 0x7f26820fb700 from 0x7f2680ef2700 | |
Pkilling 0x7f26822fc700 from 0x7f2680ef2700 | |
Pkilling 0x7f26824fd700 from 0x7f2680ef2700 | |
Pkilling 0x7f268d330780 from 0x7f2680ef2700 | |
Pkilling 0x7f26828ff700 from 0x7f2680ef2700 | |
Pkilling 0x7f268ceab700 from 0x7f2680ef2700 | |
Pkilling 0x7f239cef8700 from 0x7f2680ef2700 | |
Pkilling 0x7f2681efa700 from 0x7f2680ef2700 | |
Entering thread summarizer pause from 0x7f2680ef2700 | |
Finished thread summarizer pause from 0x7f2680ef2700. | |
jit_tls required for stack walk | |
Waiting for dumping threads to resume | |
Didn't have permission to access mono_crash.0.0.json for file dump | |
Didn't have permission to access mono_crash.0.1.json for file dump | |
Didn't have permission to access mono_crash.0.2.json for file dump | |
Didn't have permission to access mono_crash.0.3.json for file dump | |
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Didn't have permission to access mono_crash.0.5.json for file dump | |
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Didn't have permission to access mono_crash.0.11.json for file dump | |
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Didn't have permission to access mono_crash.0.45.json for file dump | |
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Didn't have permission to access mono_crash.0.49.json for file dump | |
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Didn't have permission to access mono_crash.0.89.json for file dump | |
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Didn't have permission to access mono_crash.0.99.json for file dump | |
Debug info from gdb: | |
mono_gdb_render_native_backtraces not supported on this platform, unable to find gdb or lldb | |
================================================================= | |
Got a SIGABRT while executing native code. This usually indicates | |
a fatal error in the mono runtime or one of the native libraries | |
used by your application. | |
================================================================= | |
Unhandled Exception: | |
System.Exception: Exception during execution of external process: 49404 | |
at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternal (System.Int32 taskIndex, System.Int32 threadIndex) [0x000f2] in <889c264bcadd48e1bc1fdbf91f7ed89e>:0 | |
at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0000c] in <889c264bcadd48e1bc1fdbf91f7ed89e>:0 | |
at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <889c264bcadd48e1bc1fdbf91f7ed89e>:0 | |
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <1a28d678f56741a1893be934d35463ed>:0 | |
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 49404 | |
at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternal (System.Int32 taskIndex, System.Int32 threadIndex) [0x000f2] in <889c264bcadd48e1bc1fdbf91f7ed89e>:0 | |
at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0000c] in <889c264bcadd48e1bc1fdbf91f7ed89e>:0 | |
at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <889c264bcadd48e1bc1fdbf91f7ed89e>:0 | |
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <1a28d678f56741a1893be934d35463ed>:0 | |
at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <1a28d678f56741a1893be934d35463ed>:0 |
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$ uname -rm | |
4.18.16-arch1-1-ARCH x86_64 | |
$ mono --version | |
Mono JIT compiler version 5.16.0 (makepkg/6e48ad4f7b1 Mon Oct 15 22:56:48 CEST 2018) | |
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com | |
TLS: __thread | |
SIGSEGV: altstack | |
Notifications: epoll | |
Architecture: amd64 | |
Disabled: none | |
Misc: softdebug | |
Interpreter: yes | |
LLVM: supported, not enabled. | |
GC: sgen (concurrent by default) | |
$ maxquant --version | |
MaxQuantCmd 1.6.3.3 | |
$ maxquant -p 20 -e 38 mqpar.xml | |
Applying FDR | |
Stacktrace: | |
at <unknown> <0xffffffff> | |
at (wrapper managed-to-native) object.__icall_wrapper_mono_gc_alloc_obj (intptr,intptr) [0x00000] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
at (wrapper alloc) object.AllocSmall (intptr,intptr) <0x000eb> | |
at MsLib.Search.AndromedaPeptide..ctor (System.IO.BinaryReader) [0x00055] in <55b3e077616e46b583233307c426d434>:0 | |
at MaxQuantPLibS.Search.Identifications.Read () [0x000c7] in <bf85706eecb348938b85bf6849ffe5db>:0 | |
at MaxQuantPLibS.Search.Identifications.get_Count () [0x0000f] in <bf85706eecb348938b85bf6849ffe5db>:0 | |
at MaxQuantPLibS.Search.AndromedaEnhancement.Correct1 (MsLib.Util.QueryType,System.Collections.Generic.ICollection`1<bool>,System.Collections.Generic.ICollection`1<double>,System.Collections.Generic.ICollection`1<System.Tuple`5<MsLib.Search.ModificationKey, int16, int16, byte, bool>>,MaxQuantPLibS.Basic.GroupParams,bool,string,bool,bool) [0x00016] in <bf85706eecb348938b85bf6849ffe5db>:0 | |
at MaxQuantPLibS.Search.AndromedaEnhancement/<>c__DisplayClass34_0.<CorrectNmodsNcleave>b__0 (int) [0x00057] in <bf85706eecb348938b85bf6849ffe5db>:0 | |
at BaseLibS.Util.ThreadDistributor/<>c__DisplayClass15_0.<.ctor>b__0 (int,int) [0x00000] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at BaseLibS.Util.ThreadDistributor.Work (object) [0x00067] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at System.Threading.ThreadHelper.ThreadStart_Context (object) [0x00025] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext,System.Threading.ContextCallback,object,bool) [0x00071] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext,System.Threading.ContextCallback,object,bool) [0x00000] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext,System.Threading.ContextCallback,object) [0x0002b] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
at System.Threading.ThreadHelper.ThreadStart (object) [0x0000f] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
at (wrapper runtime-invoke) <Module>.runtime_invoke_void__this___object (object,intptr,intptr,intptr) [0x0004f] in <c6745222adcf4e3f90bbf18e4a1af3ac>:0 | |
/proc/self/maps: | |
40114000-40124000 rwxp 00000000 00:00 0 | |
41667000-416d7000 rwxp 00000000 00:00 0 | |
55c423350000-55c42337a000 r--p 00000000 00:16 503691 /usr/bin/mono-sgen | |
55c42337a000-55c42366b000 r-xp 0002a000 00:16 503691 /usr/bin/mono-sgen | |
55c42366b000-55c423790000 r--p 0031b000 00:16 503691 /usr/bin/mono-sgen | |
55c423791000-55c423798000 r--p 00440000 00:16 503691 /usr/bin/mono-sgen | |
55c423798000-55c42379d000 rw-p 00447000 00:16 503691 /usr/bin/mono-sgen | |
55c42379d000-55c4237b3000 rw-p 00000000 00:00 0 | |
55c424287000-55c424904000 rw-p 00000000 00:00 0 [heap] | |
7f8ef8640000-7f8ef86c0000 rw-p 00000000 00:00 0 | |
7f8ef86c4000-7f8ef8744000 rw-p 00000000 00:00 0 | |
7f8ef8748000-7f8ef87c8000 rw-p 00000000 00:00 0 | |
7f8ef87cc000-7f8ef884c000 rw-p 00000000 00:00 0 | |
7f8ef8850000-7f8ef88d0000 rw-p 00000000 00:00 0 | |
7f8ef88d4000-7f8ef8954000 rw-p 00000000 00:00 0 | |
7f8ef8958000-7f8ef89d8000 rw-p 00000000 00:00 0 | |
7f8ef89dc000-7f8ef8a5c000 rw-p 00000000 00:00 0 | |
7f8ef8a60000-7f8ef8ae0000 rw-p 00000000 00:00 0 | |
7f8ef8ae4000-7f8ef8b64000 rw-p 00000000 00:00 0 | |
7f8ef8b68000-7f8ef8be8000 rw-p 00000000 00:00 0 | |
7f8ef8bec000-7f8ef8c6c000 rw-p 00000000 00:00 0 | |
7f8ef8c70000-7f8ef8cf0000 rw-p 00000000 00:00 0 | |
7f8ef8cf4000-7f8ef8d74000 rw-p 00000000 00:00 0 | |
7f8ef8d78000-7f8ef8df8000 rw-p 00000000 00:00 0 | |
7f8ef8dfc000-7f8ef8e7c000 rw-p 00000000 00:00 0 |
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$ uname -rm | |
4.18.16-arch1-1-ARCH x86_64 | |
$ mono --version | |
Mono JIT compiler version 5.21.0 (master/adc72216b38 Tue Oct 30 13:25:21 CET 2018) | |
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com | |
TLS: __thread | |
SIGSEGV: altstack | |
Notifications: epoll | |
Architecture: amd64 | |
Disabled: none | |
Misc: softdebug | |
Interpreter: yes | |
LLVM: supported, not enabled. | |
Suspend: hybrid | |
GC: sgen (concurrent by default) | |
$ maxquant --version | |
MaxQuantCmd 1.6.3.3 | |
$ maxquant -p 20 -e 38 mqpar.xml | |
Applying FDR | |
Error: Garbage collector could not allocate 16384 bytes of memory for major heap section. | |
Unhandled Exception: | |
System.Exception: Exception during execution of external process: 95183 | |
at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0013b] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001c] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <004736cb09e745a188841831b0bf9286>:0 | |
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 95183 | |
at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0013b] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001c] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <b8c34d2ac5944dd7a80ca5910497b476>:0 | |
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <004736cb09e745a188841831b0bf9286>:0 | |
at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <004736cb09e745a188841831b0bf9286>:0 |
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That was my problem -- I had to bring this to the attention of our HPC team, who fixed it (but I had to wait some weeks for the fix as machine restarts were required). I found no other solution, sorry.