"3dmaskave': munmap_chunk(): invalid pointer" error

jaipel · October 14, 2016, 9:51pm

One of the end-users of our software package (which depends upon AFNI) is encountering the following error while running 3dmaskave:

*** Error in `3dmaskave’: munmap_chunk(): ======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x77725)[0x7ff70c2bc /lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7ff70c 3dmaskave[0x4482e6]
3dmaskave[0x40bd3c]
3dmaskave[0x747d34]
3dmaskave[0x57ad44]
3dmaskave[0x528527]
3dmaskave[0x4a24f0]
3dmaskave[0x4b093d]
3dmaskave[0x40a428]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf 3dmaskave[0x407ca9]
======= Memory map: ========
00400000-0088f000 r-xp 00000000 08:05 272835 00a8e000-00ad8000 rw-p 0048e000 08:05 272835 00ad8000-00b0f000 rw-p 00000000 00:00 0
00d74000-00d95000 rw-p 00000000 00:00 0 7ff70acc1000-7ff70acd7000 r-xp 00000000 08:05 2898119 7ff70acd7000-7ff70aed6000 —p 00016000 08:05 2898119 7ff70aed6000-7ff70aed7000 rw-p 00015000 08:05 2898119 7ff70aed7000-7ff70aedc000 r-xp 00000000 08:05 3154309 7ff70aedc000-7ff70b0db000 —p 00005000 08:05 3154309 7ff70b0db000-7ff70b0dc000 r–p 00004000 08:05 3154309 7ff70b0dc000-7ff70b0dd000 rw-p 00005000 08:05 3154309 7ff70b0dd000-7ff70b0f5000 r-xp 00000000 08:05 2898175 7ff70b0f5000-7ff70b2f4000 —p 00018000 08:05 2898175 7ff70b2f4000-7ff70b2f5000 r–p 00017000 08:05 2898175 7ff70b2f5000-7ff70b2f6000 rw-p 00018000 08:05 2898175 7ff70b2f6000-7ff70b2fa000 rw-p 00000000 00:00 0
7ff70b2fa000-7ff70b320000 r-xp 00000000 08:05 2898418 7ff70b320000-7ff70b520000 —p 00026000 08:05 2898418 7ff70b520000-7ff70b522000 r–p 00026000 08:05 2898418 7ff70b522000-7ff70b523000 rw-p 00028000 08:05 2898418 7ff70b523000-7ff70b544000 r-xp 00000000 08:05 3155694 7ff70b544000-7ff70b743000 —p 00021000 08:05 3155694 7ff70b743000-7ff70b744000 r–p 00020000 08:05 3155694 7ff70b744000-7ff70b745000 rw-p 00021000 08:05 3155694 7ff70b745000-7ff70b749000 r-xp 00000000 08:05 2887485 7ff70b749000-7ff70b948000 —p 00004000 08:05 2887485 7ff70b948000-7ff70b949000 r–p 00003000 08:05 2887485 7ff70b949000-7ff70b94a000 rw-p 00004000 08:05 2887485 7ff70b94a000-7ff70b94c000 r-xp 00000000 08:05 3154298 invalid pointer: 0x0000000000d7f830 ***
725]
2c8c18]
0)[0x7ff70c265830]
/opt/afni/3dmaskave
/opt/afni/3dmaskave
[heap]
/lib/x86_64-linux-gnu/libgcc_s.so.1
/lib/x86_64-linux-gnu/libgcc_s.so.1
/lib/x86_64-linux-gnu/libgcc_s.so.1
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
/lib/x86_64-linux-gnu/libpthread-2.23.so
/lib/x86_64-linux-gnu/libpthread-2.23.so
/lib/x86_64-linux-gnu/libpthread-2.23.so
/lib/x86_64-linux-gnu/libpthread-2.23.so
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
/usr/lib/x86_64-linux-gnu/libXau

Based on previous posts here, we’ve checked that there is enough memory available to run 3dmaskave, and it doesn’t seem that adding “AFNI_NOMMAP=YES” to the user’s .bashrc file worked either. The issue looks like it might lie in the path name length for the two inputs that are being fed into 3dmaskave, but I manually tried running 3dmaskave on two different inputs with the exact same path names and didn’t encounter the same issue.

Any help in diagnosing this behavior would be greatly appreciated. More details can be found on the end-user’s post on our forum here.

nimzodisaster · October 14, 2016, 11:05pm

I received this error using:
Precompiled binary linux_openmp_64: May 11 2016 (Version AFNI_16.1.15)

rickr · October 15, 2016, 1:15am

By “I”, do you mean you are the end user actually
running into this problem?

If so, are you able to duplicate that error with a
3dmaskave command at the command line?

Again, if so, would you please add the option:

-DAFNI_NOMMAP=YES

to the command and see whether that helps?
e.g. 3dmaskave -DAFNI_NOMMAP=YES -mask …

I do not think adding it to the .bashrc file will
help until you actually logout and log back in.

On a related note, are you running the program
on a remotely mounted file system (e.g. NFS)?

Thanks,

rick

nimzodisaster · October 17, 2016, 1:05am

Hi,

This is being computed on a local filesystem.

Here is the command and output with your added flag.

gose66@:~/…/tmp$ 3dmaskave -DAFNI_NOMMAP=YES -mask /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/wrk/group_analysis/IMFAR_ALL_InteractionEffects/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd__scan_func_108567-100_1.func_f/__csf_threshold_096__gm_threshold_07__wm_threshold_096__threshold_0251__compcor_ncomponents_5_selector_pc10linear0wm1global1motion1quadratic0gm0compcor0csf1__bandpass_freqs_0008008__mask_rois_2mm__fwhm_6__fisher_z_score1/merged_files/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd_merged_mask.nii.gz /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/out/pipeline_preprocAll/111622-100/sca_roi_files_to_standard_smooth_fisher_zstd/_scan_func_111622-100.func_f/_csf_threshold_0.96/_gm_threshold_0.7/_wm_threshold_0.96/_threshold_0.251/_compcor_ncomponents_5_selector_pc10.linear0.wm1.global1.motion1.quadratic0.gm0.compcor0.csf1/_bandpass_freqs_0.008.0.08/_mask_rois_2mm/_fwhm_6/_fisher_z_score1/sca_roi_2_antswarp_maths_fisher_zstd.nii.gz
++ 3dmaskave: AFNI version=AFNI_16.1.15 (May 11 2016) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/wrk/group_analysis/IMFAR_ALL_InteractionEffects/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd__scan_func_108567-100_1.func_f/__csf_threshold_096__gm_threshold_07__wm_threshold_096__threshold_0251__compcor_ncomponents_5_selector_pc10linear0wm1global1motion1quadratic0gm0compcor0csf1__bandpass_freqs_0008008__mask_rois_2mm__fwhm_6__fisher_z_score1/merged_files/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd_merged_mask.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
*** Error in `3dmaskave’: munmap_chunk(): invalid pointer: 0x0000000001a3fae0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x77725)[0x7fe268e21725]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fe268e2dc18]
3dmaskave[0x4482e6]
3dmaskave[0x40bd3c]
3dmaskave[0x747d34]
3dmaskave[0x57ad44]
3dmaskave[0x528527]
3dmaskave[0x4a24f0]
3dmaskave[0x4b093d]
3dmaskave[0x40a428]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fe268dca830]
3dmaskave[0x407ca9]
======= Memory map: ========
00400000-0088f000 r-xp 00000000 08:05 272835 /opt/afni/3dmaskave
00a8e000-00ad8000 rw-p 0048e000 08:05 272835 /opt/afni/3dmaskave
00ad8000-00b0f000 rw-p 00000000 00:00 0
01a34000-01a55000 rw-p 00000000 00:00 0 [heap]
7fe267826000-7fe26783c000 r-xp 00000000 08:05 2898119 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe26783c000-7fe267a3b000 —p 00016000 08:05 2898119 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe267a3b000-7fe267a3c000 rw-p 00015000 08:05 2898119 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe267a3c000-7fe267a41000 r-xp 00000000 08:05 3154309 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fe267a41000-7fe267c40000 —p 00005000 08:05 3154309 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fe267c40000-7fe267c41000 r–p 00004000 08:05 3154309 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fe267c41000-7fe267c42000 rw-p 00005000 08:05 3154309 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7fe267c42000-7fe267c5a000 r-xp 00000000 08:05 2898175 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe267c5a000-7fe267e59000 —p 00018000 08:05 2898175 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe267e59000-7fe267e5a000 r–p 00017000 08:05 2898175 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe267e5a000-7fe267e5b000 rw-p 00018000 08:05 2898175 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe267e5b000-7fe267e5f000 rw-p 00000000 00:00 0
7fe267e5f000-7fe267e85000 r-xp 00000000 08:05 2898418 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fe267e85000-7fe268085000 —p 00026000 08:05 2898418 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fe268085000-7fe268087000 r–p 00026000 08:05 2898418 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fe268087000-7fe268088000 rw-p 00028000 08:05 2898418 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7fe268088000-7fe2680a9000 r-xp 00000000 08:05 3155694 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fe2680a9000-7fe2682a8000 —p 00021000 08:05 3155694 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fe2682a8000-7fe2682a9000 r–p 00020000 08:05 3155694 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fe2682a9000-7fe2682aa000 rw-p 00021000 08:05 3155694 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fe2682aa000-7fe2682ae000 r-xp 00000000 08:05 2887485 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fe2682ae000-7fe2684ad000 —p 00004000 08:05 2887485 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fe2684ad000-7fe2684ae000 r–p 00003000 08:05 2887485 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fe2684ae000-7fe2684af000 rw-p 00004000 08:05 2887485 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7fe2684af000-7fe2684b1000 r-xp 00000000 08:05 3154298 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fe2684b1000-7fe2686b1000 —p 00002000 08:05 3154298 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fe2686b1000-7fe2686b2000 r–p 00002000 08:05 3154298 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fe2686b2000-7fe2686b3000 rw-p 00003000 08:05 3154298 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fe2686b3000-7fe2686bc000 r-xp 00000000 08:05 3154331 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fe2686bc000-7fe2688bb000 —p 00009000 08:05 3154331 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fe2688bb000-7fe2688bc000 r–p 00008000 08:05 3154331 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fe2688bc000-7fe2688bd000 rw-p 00009000 08:05 3154331 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7fe2688bd000-7fe268961000 r-xp 00000000 08:05 3154747 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fe268961000-7fe268b60000 —p 000a4000 08:05 3154747 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fe268b60000-7fe268b66000 r–p 000a3000 08:05 3154747 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fe268b66000-7fe268b67000 rw-p 000a9000 08:05 3154747 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1
7fe268b67000-7fe268ba4000 r-xp 00000000 08:05 3146112 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fe268ba4000-7fe268da3000 —p 0003d000 08:05 3146112 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fe268da3000-7fe268da5000 r–p 0003c000 08:05 3146112 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fe268da5000-7fe268daa000 rw-p 0003e000 08:05 3146112 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.9.0
7fe268daa000-7fe268f6a000 r-xp 00000000 08:05 2898103 /lib/x86_64-linux-gnu/libc-2.23.so
7fe268f6a000-7fe269169000 —p 001c0000 08:05 2898103 /lib/x86_64-linux-gnu/libc-2.23.so
7fe269169000-7fe26916d000 r–p 001bf000 08:05 2898103 /lib/x86_64-linux-gnu/libc-2.23.so
7fe26916d000-7fe26916f000 rw-p 001c3000 08:05 2898103 /lib/x86_64-linux-gnu/libc-2.23.so
7fe26916f000-7fe269173000 rw-p 00000000 00:00 0
7fe269173000-7fe269176000 r-xp 00000000 08:05 2898112 /lib/x86_64-linux-gnu/libdl-2.23.so
7fe269176000-7fe269375000 —p 00003000 08:05 2898112 /lib/x86_64-linux-gnu/libdl-2.23.so
7fe269375000-7fe269376000 r–p 00002000 08:05 2898112 /lib/x86_64-linux-gnu/libdl-2.23.so
7fe269376000-7fe269377000 rw-p 00003000 08:05 2898112 /lib/x86_64-linux-gnu/libdl-2.23.so
7fe269377000-7fe26947f000 r-xp 00000000 08:05 2898134 /lib/x86_64-linux-gnu/libm-2.23.so
7fe26947f000-7fe26967e000 —p 00108000 08:05 2898134 /lib/x86_64-linux-gnu/libm-2.23.so
7fe26967e000-7fe26967f000 r–p 00107000 08:05 2898134 /lib/x86_64-linux-gnu/libm-2.23.so
7fe26967f000-7fe269680000 rw-p 00108000 08:05 2898134 /lib/x86_64-linux-gnu/libm-2.23.so
7fe269680000-7fe269699000 r-xp 00000000 08:05 2898199 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fe269699000-7fe269898000 —p 00019000 08:05 2898199 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fe269898000-7fe269899000 r–p 00018000 08:05 2898199 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fe269899000-7fe26989a000 rw-p 00019000 08:05 2898199 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fe26989a000-7fe2698be000 r-xp 00000000 08:05 2898172 /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fe2698be000-7fe269abd000 —p 00024000 08:05 2898172 /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fe269abd000-7fe269abe000 r–p 00023000 08:05 2898172 /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fe269abe000-7fe269abf000 rw-p 00024000 08:05 2898172 /lib/x86_64-linux-gnu/libpng12.so.0.54.0
7fe269abf000-7fe269bf4000 r-xp 00000000 08:05 3154294 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fe269bf4000-7fe269df4000 —p 00135000 08:05 3154294 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fe269df4000-7fe269df5000 r–p 00135000 08:05 3154294 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fe269df5000-7fe269df9000 rw-p 00136000 08:05 3154294 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fe269df9000-7fe269e0f000 r-xp 00000000 08:05 3154205 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fe269e0f000-7fe26a00e000 —p 00016000 08:05 3154205 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fe26a00e000-7fe26a00f000 r–p 00015000 08:05 3154205 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fe26a00f000-7fe26a010000 rw-p 00016000 08:05 3154205 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7fe26a010000-7fe26a013000 rw-p 00000000 00:00 0
7fe26a013000-7fe26a01a000 r-xp 00000000 08:05 3154288 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fe26a01a000-7fe26a219000 —p 00007000 08:05 3154288 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fe26a219000-7fe26a21a000 r–p 00006000 08:05 3154288 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fe26a21a000-7fe26a21b000 rw-p 00007000 08:05 3154288 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7fe26a21b000-7fe26a233000 r-xp 00000000 08:05 3154323 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fe26a233000-7fe26a432000 —p 00018000 08:05 3154323 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fe26a432000-7fe26a433000 r–p 00017000 08:05 3154323 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fe26a433000-7fe26a434000 rw-p 00018000 08:05 3154323 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7fe26a434000-7fe26a445000 r-xp 00000000 08:05 3154311 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fe26a445000-7fe26a644000 —p 00011000 08:05 3154311 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fe26a644000-7fe26a645000 r–p 00010000 08:05 3154311 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fe26a645000-7fe26a646000 rw-p 00011000 08:05 3154311 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7fe26a646000-7fe26a656000 r-xp 00000000 08:05 3154327 /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fe26a656000-7fe26a855000 —p 00010000 08:05 3154327 /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fe26a855000-7fe26a856000 r–p 0000f000 08:05 3154327 /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fe26a856000-7fe26a857000 rw-p 00010000 08:05 3154327 /usr/lib/x86_64-linux-gnu/libXpm.so.4.11.0
7fe26a857000-7fe26a85f000 r-xp 00000000 08:05 3146093 /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7fe26a85f000-7fe26aa5e000 —p 00008000 08:05 3146093 /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7fe26aa5e000-7fe26aa5f000 r–p 00007000 08:05 3146093 /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7fe26aa5f000-7fe26aa60000 rw-p 00008000 08:05 3146093 /usr/lib/x86_64-linux-gnu/libXp.so.6.2.0
7fe26aa60000-7fe26aa74000 r-xp 00000000 08:05 3154317 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fe26aa74000-7fe26ac73000 —p 00014000 08:05 3154317 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fe26ac73000-7fe26ac74000 r–p 00013000 08:05 3154317 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fe26ac74000-7fe26ac75000 rw-p 00014000 08:05 3154317 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.2
7fe26ac75000-7fe26acd7000 r-xp 00000000 08:05 3154335 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fe26acd7000-7fe26aed7000 —p 00062000 08:05 3154335 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fe26aed7000-7fe26aed8000 r–p 00062000 08:05 3154335 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fe26aed8000-7fe26aedd000 rw-p 00063000 08:05 3154335 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7fe26aedd000-7fe26aede000 rw-p 00000000 00:00 0
7fe26aede000-7fe26af04000 r-xp 00000000 08:05 2898089 /lib/x86_64-linux-gnu/ld-2.23.so
7fe26b0c4000-7fe26b0d0000 rw-p 00000000 00:00 0
7fe26b100000-7fe26b103000 rw-p 00000000 00:00 0
7fe26b103000-7fe26b104000 r–p 00025000 08:05 2898089 /lib/x86_64-linux-gnu/ld-2.23.so
7fe26b104000-7fe26b105000 rw-p 00026000 08:05 2898089 /lib/x86_64-linux-gnu/ld-2.23.so
7fe26b105000-7fe26b106000 rw-p 00000000 00:00 0
7ffccd022000-7ffccd044000 rw-p 00000000 00:00 0 [stack]
7ffccd132000-7ffccd134000 r–p 00000000 00:00 0 [vvar]
7ffccd134000-7ffccd136000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

Fatal Signal 6 (SIGABRT) received
Last STATUS: free im
mri_free
THD_init_datablock_brick
EDIT_dset_items
THD_open_nifti
THD_open_one_dataset
THD_open_dataset
3dmaskave main
Bottom of Debug Stack
** Command line was:
3dmaskave -mask /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/wrk/group_analysis/IMFAR_ALL_InteractionEffects/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd__scan_func_108567-100_1.func_f/__csf_threshold_096__gm_threshold_07__wm_threshold_096__threshold_0251__compcor_ncomponents_5_selector_pc10linear0wm1global1motion1quadratic0gm0compcor0csf1__bandpass_freqs_0008008__mask_rois_2mm__fwhm_6__fisher_z_score1/merged_files/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd_merged_mask.nii.gz /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/out/pipeline_preprocAll/111622-100/sca_roi_files_to_standard_smooth_fisher_zstd/_scan_func_111622-100.func_f/_csf_threshold_0.96/_gm_threshold_0.7/_wm_threshold_0.96/_threshold_0.251/_compcor_ncomponents_5_selector_pc10.linear0.wm1.global1.motion1.quadratic0.gm0.compcor0.csf1/_bandpass_freqs_0.008.0.08/_mask_rois_2mm/_fwhm_6/_fisher_z_score1/sca_roi_2_antswarp_maths_fisher_zstd.nii.gz
** AFNI version = AFNI_16.1.15 Compile date = May 11 2016
** [[Precompiled binary linux_openmp_64: May 11 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/gose66/.afni.crashlog

→
HOWEVER, if I copy both of the input files to the current directory, and run the command on these files, 3dmaskave works perfectly. --THis makes me suspect path length.

rickr · October 17, 2016, 12:48pm

I agree about the path length, thanks for testing
the copied files, both of you. We do have some
compiled limits on file name lengths.

Is this an outlier in terms of the long path? Or
would you expect this to be a little common,
even if only in within C-PAC?

Thanks,

rick

rwcox · October 17, 2016, 4:04pm

This is peculiar – the filename lengths (about 570 characters) are not overly long for AFNI. Can you get the crashlog for this from /home/gose66/.afni.crashlog and email it to me?

nimzodisaster · October 17, 2016, 5:33pm

crashlog:

------ CRASH LOG ------------------------------**
Fatal Signal 6 (SIGABRT) received
… recent internal history …
THD_init_datablock_brick – making new dblk->brick
THD_init_datablock_brick – starting sub-brick creations
++++++++mri_new_7D_generic [8]: {ENTRY (file=mri_new.c line=48) from THD_init_datablock_brick
--------mri_new_7D_generic [8]: EXIT} (file=mri_new.c line=140) to THD_init_datablock_brick
THD_init_datablock_brick – exiting
-------THD_init_datablock_brick [7]: EXIT} (file=thd_initdblk.c line=1268) to EDIT_empty_copy
------EDIT_empty_copy [6]: EXIT} (file=edt_emptycopy.c line=227) to THD_open_nifti
++++++THD_init_diskptr_names [6]: {ENTRY (file=thd_initdkptr.c line=27) from THD_open_nifti
------THD_init_diskptr_names [6]: EXIT} (file=thd_initdkptr.c line=148) to THD_open_nifti
++++++EDIT_dset_items [6]: {ENTRY (file=edt_dsetitems.c line=125) from THD_open_nifti
+++++++storage_mode_from_prefix [7]: {ENTRY (file=thd_opendset.c line=599) from EDIT_dset_items
++++++++storage_mode_from_filename [8]: {ENTRY (file=thd_opendset.c line=526) from storage_mode_from_prefix
--------storage_mode_from_filename [8]: EXIT} (file=thd_opendset.c line=555) to storage_mode_from_prefix
-------storage_mode_from_prefix [7]: EXIT} (file=thd_opendset.c line=603) to EDIT_dset_items
+++++++AFNI_process_environ [7]: {ENTRY (file=afni_environ.c line=112) from EDIT_dset_items
++++++++AFNI_suck_file [8]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
--------AFNI_suck_file [8]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
-------AFNI_process_environ [7]: EXIT} (file=afni_environ.c line=132) to EDIT_dset_items
+++++++THD_init_diskptr_names [7]: {ENTRY (file=thd_initdkptr.c line=27) from EDIT_dset_items
-------THD_init_diskptr_names [7]: EXIT} (file=thd_initdkptr.c line=148) to EDIT_dset_items
+++++++storage_mode_from_filename [7]: {ENTRY (file=thd_opendset.c line=526) from EDIT_dset_items
-------storage_mode_from_filename [7]: EXIT} (file=thd_opendset.c line=555) to EDIT_dset_items
+++++++THD_init_datablock_brick [7]: {ENTRY (file=thd_initdblk.c line=1206) from EDIT_dset_items
THD_init_datablock_brick – destroying old dblk->brick
++++++++mri_free [8]: {ENTRY (file=mri_free.c line=49) from THD_init_datablock_brick
mri_free – call killpurge
+++++++++mri_killpurge [9]: {ENTRY (file=mri_purger.c line=259) from mri_free
mri_killpurge – check if im==NULL ptr=0x20faae0
mri_killpurge – can’t killpurge NULL fname!
---------mri_killpurge [9]: EXIT} (file=mri_purger.c line=270) to mri_free
mri_free – free im
…
** Command line was:
3dmaskave -mask /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/wrk/group_analysis/IMFAR_ALL_InteractionEffects/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd__scan_func_108567-100_1.func_f/__csf_threshold_096__gm_threshold_07__wm_threshold_096__threshold_0251__compcor_ncomponents_5_selector_pc10linear0wm1global1motion1quadratic0gm0compcor0csf1__bandpass_freqs_0008008__mask_rois_2mm__fwhm_6__fisher_z_score1/merged_files/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd_merged_mask.nii.gz /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/out/pipeline_preprocAll/111622-100/sca_roi_files_to_standard_smooth_fisher_zstd/_scan_func_111622-100.func_f/_csf_threshold_0.96/_gm_threshold_0.7/_wm_threshold_0.96/_threshold_0.251/_compcor_ncomponents_5_selector_pc10.linear0.wm1.global1.motion1.quadratic0.gm0.compcor0.csf1/_bandpass_freqs_0.008.0.08/_mask_rois_2mm/_fwhm_6/_fisher_z_score1/sca_roi_2_antswarp_maths_fisher_zstd.nii.gz
…
Last STATUS: free im
mri_free
THD_init_datablock_brick
EDIT_dset_items
THD_open_nifti
THD_open_one_dataset
THD_open_dataset
3dmaskave main
** Command line was:
3dmaskave -mask /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/wrk/group_analysis/IMFAR_ALL_InteractionEffects/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd__scan_func_108567-100_1.func_f/__csf_threshold_096__gm_threshold_07__wm_threshold_096__threshold_0251__compcor_ncomponents_5_selector_pc10linear0wm1global1motion1quadratic0gm0compcor0csf1__bandpass_freqs_0008008__mask_rois_2mm__fwhm_6__fisher_z_score1/merged_files/sca_roi_files_to_standard_smooth_fisher_zstd__mask_rois_2mm_sca_roi_2_antswarp_maths_fisher_zstd_merged_mask.nii.gz /home/gose66/RestingState/PROJECTS/MIND/PRIMARY/out/pipeline_preprocAll/111622-100/sca_roi_files_to_standard_smooth_fisher_zstd/_scan_func_111622-100.func_f/_csf_threshold_0.96/_gm_threshold_0.7/_wm_threshold_0.96/_threshold_0.251/_compcor_ncomponents_5_selector_pc10.linear0.wm1.global1.motion1.quadratic0.gm0.compcor0.csf1/_bandpass_freqs_0.008.0.08/_mask_rois_2mm/_fwhm_6/_fisher_z_score1/sca_roi_2_antswarp_maths_fisher_zstd.nii.gz
** AFNI compile date = May 11 2016
** [[Precompiled binary linux_openmp_64: May 11 2016]]
** Program Crash **

rwcox · October 17, 2016, 7:36pm

Okay, the problem is obvious. The max filename allowed currently is 511 characters. Somewhere in the screen output before the crash should be a cryptic message like

** ERROR: Path name too long. Returning ‘./’

We will increase the max filename length, and even improve the error message. But ultimately there is a limit to the absurdity of filename paths that we will be able to handle.

– bob cox

nimzodisaster · October 17, 2016, 8:10pm

Thanks Bob,
Joshua Lee