Segmentation Faults when Running MEX files in Parallel

I am currently running repetitions of an experiment that uses MEX files in MATLAB 2012a and occasionally running into segmentation faults that I cannot understand.

Some information about the faults

- They occur randomly

- They only occur when I run multiple repetitions of my experiment in parallel on a Linux machine using a parfor loop.

- They do not occur when I run the repeitions of my experiment in parallel on my Mac using a parfor loop.

- They do not occur when I run or do they occur whenThey do not occur when I run the repetitions sequentially.

- They appear to occur far less frequently when I run 2 experiments in parallel - as opposed to 12 experiments in parallel.

- They occur in MATLAB 2011b and 2012a...

Some information about my MEX file:

- It is written in C

- It uses the IBM CPLEX 12.4 API (this is thread-safe)

- It was compiled using GCC 4.6.3

My thoughts are that there may be some kind of file access issue. Can anyone shed any light on what might be going on? I'd be happy to provide more information as necessary.

[Jill Reese]

Could you post the code from the parfor loop? Is there a stack trace from the seg fault? What steps did you go through to compile the MEX file?

[Berk Ustun]

The code inside the parfor loop is very basic, and essentially has the following form

results = cell(1,30) % a 30 x 1 cell to store output data

settings = %a 30 x 1 cell with settings for each experiment

parfor i = 1:30

results{i} = myExperiment(settings{i})

end

[Berk Ustun]

I'm including a Stack Trace below:

------------------------------------------------------------------------

Segmentation violation detected at Tue Apr 17 21:40:34 2012

------------------------------------------------------------------------

Configuration:

Crash Decoding : Disabled

Current Visual : None

Default Encoding: UTF-8

GNU C Library : 2.14.90 development

MATLAB Root : /home/software/matlab/matlab-2012a

MATLAB Version : 7.14.0.739 (R2012a)

Operating System: Linux 3.3.1-3.fc16.x86_64 #1 SMP Wed Apr 4 18:08:51 UTC 2012 x86_64

Processor ID : x86 Family 6 Model 44 Stepping 2, GenuineIntel

Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode

Window System : No active display

Fault Count: 1

Abnormal termination:

Segmentation violation

Register State (from fault):

RAX = 0000000000000000 RBX = 0000000000000011

RCX = 0000000000000010 RDX = 0000000000000011

RSP = 00007f32661f2f08 RBP = 00007f32661f2f80

RSI = 00007f32661f2f90 RDI = 00007f319f9ada40

R8 = 000000000000ffff R9 = 0000000000000060

R10 = 00000032f0089fa0 R11 = 0000000000000011

R12 = 00007f32661f2f90 R13 = 00007f319f9ada40

R14 = 0000000000000050 R15 = 00000032f03b4598

RIP = 00000032f0088acc EFL = 0000000000010283

CS = 0033 FS = 0000 GS = 0000

Stack Trace (from fault):

[ 0] 0x00007f327e62c92e /home/software/matlab/matlab-2012a/bin/glnxa64/libmwfl.so+00370990 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000158

[ 1] 0x00007f327e62f7d0 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwfl.so+00382928

[ 2] 0x00007f327e62fb3b /home/software/matlab/matlab-2012a/bin/glnxa64/libmwfl.so+00383803 _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextE+000171

[ 3] 0x00007f327d511203 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01253891 _ZN2fl4diag13terminate_logEPKcPK8ucontext+000067

[ 4] 0x00007f327d50e0fd /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01241341

[ 5] 0x00007f327d50f79d /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01247133

[ 6] 0x00007f327d50f925 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01247525

[ 7] 0x00007f327d50ff01 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01249025

[ 8] 0x00007f327d5103f5 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01250293

[ 9] 0x00000032f0c0f500 /lib64/libpthread.so.0+00062720

[ 10] 0x00000032f0088acc /lib64/libc.so.6+00559820

[ 11] 0x00000032f003915a /lib64/libc.so.6+00233818

[ 12] 0x00000032f003903d /lib64/libc.so.6+00233533 putenv+000109

[ 13] 0x00007f31a71fc676 /home/software/cplex/cplex-12.4/cplex/matlab/cplexlink124.mexa64+02860662

[ 14] 0x00007f31a7008434 /home/software/cplex/cplex-12.4/cplex/matlab/cplexlink124.mexa64+00812084

[ 15] 0x00007f31a7007af4 /home/software/cplex/cplex-12.4/cplex/matlab/cplexlink124.mexa64+00809716

[ 16] 0x00007f31a700730c /home/software/cplex/cplex-12.4/cplex/matlab/cplexlink124.mexa64+00807692

[ 17] 0x00007f31a6fc0c09 /home/software/cplex/cplex-12.4/cplex/matlab/cplexlink124.mexa64+00519177

[ 18] 0x00007f31a6fc0146 /home/software/cplex/cplex-12.4/cplex/matlab/cplexlink124.mexa64+00516422 mexFunction+000448

[ 19] 0x00007f3277749cca /home/software/matlab/matlab-2012a/bin/glnxa64/libmex.so+00109770 mexRunMexFile+000090

[ 20] 0x00007f3277745f79 /home/software/matlab/matlab-2012a/bin/glnxa64/libmex.so+00094073

[ 21] 0x00007f3277746de1 /home/software/matlab/matlab-2012a/bin/glnxa64/libmex.so+00097761

[ 22] 0x00007f327d1b9063 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_dispatcher.so+00479331 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000515

[ 23] 0x00007f327ca7f476 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01987702

[ 24] 0x00007f327ca30426 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01664038

[ 25] 0x00007f327ca34be4 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01682404

[ 26] 0x00007f327ca31333 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01667891

[ 27] 0x00007f327ca32037 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01671223

[ 28] 0x00007f327ca9b690 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+02102928

[ 29] 0x00007f327d1b9063 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_dispatcher.so+00479331 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000515

[ 30] 0x00007f3276366a6f /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01522287

[ 31] 0x00007f3276302124 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01110308

[ 32] 0x00007f3276302bab /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01113003

[ 33] 0x00007f3276302ebe /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01113790

[ 34] 0x00007f327630418d /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01118605

[ 35] 0x00007f32763042ad /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01118893

[ 36] 0x00007f327630454c /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01119564 _Z27omConstructObjectWithClientN4mcos9COSNameIDEiPPK11mxArray_tagPKNS_9COSClientE+000476

[ 37] 0x00007f327636f1bd /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01556925

[ 38] 0x00007f32763e9563 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+02057571

[ 39] 0x00007f327d1736a1 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_dispatcher.so+00194209 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+000481

[ 40] 0x00007f327ca7f476 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01987702

[ 41] 0x00007f327ca30426 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01664038

[ 42] 0x00007f327ca34be4 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01682404

[ 43] 0x00007f327ca31333 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01667891

[ 44] 0x00007f327ca32037 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01671223

[ 45] 0x00007f327ca9b690 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+02102928

[ 46] 0x00007f327d1b9063 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_dispatcher.so+00479331 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000515

[ 47] 0x00007f3276361388 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01500040

[ 48] 0x00007f3276302c22 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01113122

[ 49] 0x00007f3276302ebe /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01113790

[ 50] 0x00007f3276304c7c /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01121404

[ 51] 0x00007f327634d236 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01417782 _Z19omCallLoadobjMethodRN4mcos15COSInterfacePtrENS_8COSValueENS_14COSDataTypePtrE+000694

[ 52] 0x00007f327634d937 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01419575

[ 53] 0x00007f3276287676 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+00607862

[ 54] 0x00007f327633f0eb /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01360107

[ 55] 0x00007f3276330f41 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01302337

[ 56] 0x00007f32763313fe /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01303550

[ 57] 0x00007f3276332944 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308996

[ 58] 0x00007f3276332758 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308504

[ 59] 0x00007f3276332944 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308996

[ 60] 0x00007f3276332758 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308504

[ 61] 0x00007f3276332758 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308504

[ 62] 0x00007f3276332944 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308996

[ 63] 0x00007f3276334238 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01315384

[ 64] 0x00007f327633f021 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01359905

[ 65] 0x00007f3276330f41 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01302337

[ 66] 0x00007f32763313fe /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01303550

[ 67] 0x00007f3276332944 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01308996

[ 68] 0x00007f3276334238 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01315384

[ 69] 0x00007f327633f021 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01359905

[ 70] 0x00007f3276330f41 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01302337

[ 71] 0x00007f32763313fe /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01303550

[ 72] 0x00007f32763323f8 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcos.so+01307640

[ 73] 0x00007f327e37e654 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00419412

[ 74] 0x00007f327e38057a /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00427386

[ 75] 0x00007f327e37fb18 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00424728

[ 76] 0x00007f327e37fb18 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00424728

[ 77] 0x00007f327e380017 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00426007

[ 78] 0x00007f327e37fb18 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00424728

[ 79] 0x00007f327e380017 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00426007

[ 80] 0x00007f327e380017 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00426007

[ 81] 0x00007f327e380017 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00426007

[ 82] 0x00007f327e380017 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00426007

[ 83] 0x00007f327e380a23 /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00428579 miGetCurrentItem+000387

[ 84] 0x00007f327e3631db /home/software/matlab/matlab-2012a/bin/glnxa64/libmx.so+00307675 mxDeserializeWithTag+000315

[ 85] 0x00007f31bd5ba1e0 /home/software/matlab/matlab-2012a/toolbox/distcomp/distcomp/distcompdeserialize.mexa64+00008672 mexFunction+000080

[ 86] 0x00007f3277749cca /home/software/matlab/matlab-2012a/bin/glnxa64/libmex.so+00109770 mexRunMexFile+000090

[ 87] 0x00007f3277745f79 /home/software/matlab/matlab-2012a/bin/glnxa64/libmex.so+00094073

[ 88] 0x00007f3277746de1 /home/software/matlab/matlab-2012a/bin/glnxa64/libmex.so+00097761

[ 89] 0x00007f327d1b9063 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_dispatcher.so+00479331 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000515

[ 90] 0x00007f327ca7f476 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01987702

[ 91] 0x00007f327ca30426 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01664038

[ 92] 0x00007f327ca34be4 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01682404

[ 93] 0x00007f327ca31333 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01667891

[ 94] 0x00007f327ca32037 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01671223

[ 95] 0x00007f327ca9b690 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+02102928

[ 96] 0x00007f327d1b9063 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_dispatcher.so+00479331 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000515

[ 97] 0x00007f327ca5e65f /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01853023

[ 98] 0x00007f327ca5dd49 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01850697

[ 99] 0x00007f327c9bf2ec /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01200876 inCallFcnWithTrap+000092

[100] 0x00007f327ca24b6b /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01616747

[101] 0x00007f327c9be438 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwm_interpreter.so+01197112 _Z28inCallFcnWithTrapInDesiredWSiPP11mxArray_tagiS1_PKcbP15inWorkSpace_tag+000104

[102] 0x00007f3277db2d79 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwiqm.so+02485625 _ZN3iqm15BaseFEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+000457

[103] 0x00007f32546bf09d /home/software/matlab/matlab-2012a/bin/glnxa64/libnativejmi.so+00696477 _ZN9nativejmi14JmiFEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+000173

[104] 0x00007f32546f16e5 /home/software/matlab/matlab-2012a/bin/glnxa64/libnativejmi.so+00902885 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN9nativejmi14JmiFEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+000629

[105] 0x00007f3277d9b482 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwiqm.so+02389122

[106] 0x00007f3277d8c264 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwiqm.so+02327140

[107] 0x00007f327d77dafc /home/software/matlab/matlab-2012a/bin/glnxa64/libmwbridge.so+00125692 _Z10ioReadLinebP8_IO_FILEPcS1_iPbRKN5boost8optionalIKP15inWorkSpace_tagEEb+000508

[108] 0x00007f327d77e165 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwbridge.so+00127333

[109] 0x00007f327d782d0a /home/software/matlab/matlab-2012a/bin/glnxa64/libmwbridge.so+00146698

[110] 0x00007f327d783165 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwbridge.so+00147813

[111] 0x00007f327d7839ce /home/software/matlab/matlab-2012a/bin/glnxa64/libmwbridge.so+00149966 mnParser+000702

[112] 0x00007f327d4f5de2 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01142242 _ZN11mcrInstance30mnParser_on_interpreter_threadEv+000034

[113] 0x00007f327d4d851a /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01021210

[114] 0x00007f327d4d8598 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01021336

[115] 0x00007f327dd0b053 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwservices.so+00823379

[116] 0x00007f327dd0b315 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwservices.so+00824085

[117] 0x00007f327dd09bc1 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwservices.so+00818113

[118] 0x00007f3273e73605 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwuix.so+00505349

[119] 0x00007f327dd8f9a1 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwservices.so+01366433 _ZSt8for_eachIN9__gnu_cxx17__normal_iteratorIPN5boost8weak_ptrIN4sysq10ws_ppeHookEEESt6vectorIS6_SaIS6_EEEENS4_8during_FIS6_NS2_10shared_ptrIS5_EEEEET0_T_SH_SG_+000081

[120] 0x00007f327dd90aab /home/software/matlab/matlab-2012a/bin/glnxa64/libmwservices.so+01370795

[121] 0x00007f327dd8e5f9 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwservices.so+01361401 _Z25svWS_ProcessPendingEventsiib+000665

[122] 0x00007f327d4d776f /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01017711

[123] 0x00007f327d4d7c3b /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01018939

[124] 0x00007f327d4d7d97 /home/software/matlab/matlab-2012a/bin/glnxa64/libmwmcr.so+01019287

[125] 0x00000032f0c07d90 /lib64/libpthread.so.0+00032144

[126] 0x00000032f00f0f5d /lib64/libc.so.6+00986973 clone+000109

This error was detected while a MEX-file was running. If the MEX-file

is not an official MathWorks function, please examine its source code

for errors. Please consult the External Interfaces Guide for information

on debugging MEX-files.

If this problem is reproducible, please submit a Service Request via:

http://www.mathworks.com/support/contact_us/

A technical support engineer might contact you with further information.

Thank you for your help.

[Edric Ellis]

Do you see the problem if you manually launch two MATLAB processes and run your MEX file? The workers that are running the body of your PARFOR loop are essentially ordinary MATLAB processes, but launched with the '-singleCompThread' option.

[Berk Ustun]

After sending in the Stack Trace to MATLAB. It turns out that segmentation faults do originate from the thread safety, but that the function belongs to another API package that I was using in the MEX file.

Thanks for the help everyone!

[jian shulei]

I meet the same question,can you tell me how to do?

Answer 1

[James Tursa]

Do you use any MATLAB API functions that allocate or change memory, such as mxCreateDoubleMatrix, mxMalloc, etc.? These are not thread-safe in general ... I don't know specifically about how parfor deals with this. What kind of file access are you doing?

Answer 2

[Berk Ustun]

I'm actually using malloc and free instead of the MATLAB API functions so I think I should be fine on that regard.

The only file that is being accessed is the MEX file - could there be something going wrong there?

[James Tursa]

Whether malloc and free are thread-safe may depend on your implementation and compiler settings. I am not familiar with GCC.

[Berk Ustun]

Quick question: if malloc and free are thread-safe, does that imply that mxMalloc and mxFree are thread-safe?

[James Tursa]

Not necessarily. mxMalloc and mxFree *may* use malloc and friends in the background. But even if they do there is something else going on with mxMalloc and friends. MATLAB maintains a garbage collection list in the background of the addresses returned by mxMalloc & friends. The question is whether or not this garbage collection process is thread-safe or not. So the overall answer may not hinge 100% on just the thread-safeness of malloc etc.

Also, there seems to be plenty of evidence that the memory allocation/changing functions in the API are *not* thread-safe in an OpenMP environment. So the only way I can see them being thread-safe in a parfor situation is if parfor does something special in the background to interact with the mex API stuff to make it thread-safe. I really have no idea. I don't have the Parallel Toolbox to play with.

[Walter Roberson]

No, mxMalloc and mxFree are not necessarily thread-safe even when malloc and free are. mxMalloc generally works with memory that already belongs to the process and could do its housekeeping in a way that is not thread safe. mxMalloc might call malloc() when it needs more memory, but the part before and the part after that might not be thread safe.

[Berk Ustun]

Thanks for these.

My understanding is that it's generally a better idea to use malloc() and free() instead of mxMalloc and mxFree (especially if the C library is thread-safe). Is there right?

I started thinking about the other mx functions that I was using, and I'm wondering whether mxCreateDoubleMatrix / mxCreateDoubleScalar are free? If not, could I replace these functions with other functions from the C library?

[James Tursa]

If you want the MATLAB memory manager to do garbage collection for you, then you need to use mxMalloc and mxFree. Otherwise you risk memory leaks for abnormal mex function exits unless you set up your own garbage collection scheme manually.

If you are creating MATLAB mxArray variables, officially speaking you must use the API functions. While it may be possible to create an mxArray variable from scratch using malloc and hacking into the mxArray structure itself, it would be of very limited use. E.g., you couldn't return such a variable back to a MATLAB workspace ... to do so would likely crash MATLAB when it tried to free this memory with its own memory manager when in fact the memory never came from this memory manager in the first place. There would also be a host of other problems as well that I won't go into here (variable sharing, etc). You really don't want to go down this path.

Since you have the Parallel Toolbox, I would check the doc to see if there is any mention of thread-safeness of the mex MATLAB API functions in a parfor setting. If not, maybe contact technical support to see if they can give you the answer.

[James Tursa]

Another thought: Let's assume for the purposes of discussion that the mex API creation functions are not thread-safe. What you could do is create the "output" variables at the m-file level before calling the mex routine. Then pass these in as arguments and modify them in-place in the mex routine. That completely bypasses the thread-safeness issues of the mex API functions.

[Berk Ustun]

That's a great idea! Will try that out as well.