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Bug #2653

gmindist (GMX5.14, 2018 vesrions) crashes with segmentation fault

Added by Stéphane Abel about 1 year ago. Updated about 1 year ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
analysis tools
Target version:
-
Affected version - extra info:
5.1.4
Affected version:
Difficulty:
uncategorized
Close

Description

I report an issue with gmx mindist of gromacs (v 4.6.7, 5.1.4 and 2018+). The program crashes with the following command

echo 0 1 > Protein_AlkylChain.txt

  • gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n Hydratation_Protein_OGNG.ndx -b 215000 -e 215000 -dt 4 -d 0.4 -respertime -printresname -group -od 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg -on 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg < Protein_AlkylChain.txt

With GMX4.6.7 --> OK

With GMX5.1.4 (segmentation fault) ----------------------

Group 0 (Protein_HeavyAtoms) has 4976 elements
Group 1 (OGNG_AlkylChain) has 1530 elements
Group 2 ( OGNG_Headgroup) has 2244 elements
Group 3 (OGNG_All_HeavyAtoms) has 3774 elements
Group 4 ( Water_oxygen) has 60000 elements
Select a group: Select a group: ^MReading frame 0 time 0.000 ^MReading frame 0 time 200000.000
Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.2#

Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.2#
[irene1022:52095:0] Caught signal 11 (Segmentation fault) ==== backtrace ====
2 0x0000000000068d1c mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:641
3 0x000000000006926c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:616
4 0x0000000000035270 killpg() ??:0
5 0x00000000000471ad _IO_vfprintf_internal() :0
6 0x0000000000051827 __GI_fprintf() :0
7 0x00000000003b3cd8 xvgr_header() ??:0
8 0x00000000003b3c70 xvgropen_type() ??:0
9 0x0000000000545400 dist_plot.a() gmx_mindist.c:0
10 0x0000000000543990 gmx_mindist() ??:0
11 0x00000000001e1ff3 _ZN3gmx24Comman

With GMX2018 and 2018.2 (fatal error) ----------------------

Group 0 (Protein_HeavyAtoms) has 4976 elements
Group 1 (OGNG_AlkylChain) has 1530 elements
Group 2 ( OGNG_Headgroup) has 2244 elements
Group 3 (OGNG_All_HeavyAtoms) has 3774 elements
Group 4 ( Water_oxygen) has 60000 elements
Select a group: Select a group: ^MReading frame 0 time 0.000 ^MReading frame 0 time 200000.000
Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.1#

Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.1#

-------------------------------------------------------
Program: gmx mindist, version 2018
Source file: src/gromacs/fileio/gmxfio.cpp (line 345)

Fatal error:
Cannot open file with NULL filename string

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
+ echo 0 2
+ echo 0 3
+ echo 0 4
+ exit 0

Please note that if I remove the "-group" and "-printresname" arguments all the tested version (except for 4.6.7) crashes.

I have included three files for the tests

MYXTC.xtc (1 snapshot 215ns)
MYNDX.ndx
MYPDB.pdb

Thank you

MYPDB.pdb (15 MB) MYPDB.pdb PDB of the system Stéphane Abel, 09/26/2018 11:07 AM
MYXTC.xtc (715 KB) MYXTC.xtc Trajectory file (1 frame, 215 ns) Stéphane Abel, 09/26/2018 11:09 AM
MYNDX.ndx (457 KB) MYNDX.ndx index file with different subsystem Stéphane Abel, 09/26/2018 11:09 AM
MYNDX.ndx (457 KB) MYNDX.ndx index file with different subsystems Stéphane Abel, 09/26/2018 12:19 PM
MYXTC.xtc (715 KB) MYXTC.xtc Trajectory file (1 frame, 215 ns) Stéphane Abel, 09/26/2018 12:20 PM
MYPDB.pdb (15 MB) MYPDB.pdb PDB of the system Stéphane Abel, 09/26/2018 12:21 PM

Associated revisions

Revision 034183c8 (diff)
Added by Paul Bauer about 1 year ago

Add mindist output file check

gmx mindist would not check if the output file for an analysis options
was actually present, leading to cryptic error messages. Added the
corresponding check.

Fixes #2653

Change-Id: I26ccc7df37e5cc6a0276ecce50036aba452e0a45

History

#1 Updated by Stéphane Abel about 1 year ago

Below report two issues with the mindist analysis tool of gromacs (v 4.6.7, 5.1.4 and 2018+). The program crashes with the following command

gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n Hydratation_Protein_OGNG.ndx -b 200000 -e 215000 -dt 4 -d 0.4 -respertime -printresname -group -od 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg -on 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg < Protein_AlkylChain.txt

With GMX4.6.7 --> OK

With GMX5.1.4 (segmentation fault) ----------------------

Group 0 (Protein_HeavyAtoms) has 4976 elements
Group 1 (OGNG_AlkylChain) has 1530 elements
Group 2 ( OGNG_Headgroup) has 2244 elements
Group 3 (OGNG_All_HeavyAtoms) has 3774 elements
Group 4 ( Water_oxygen) has 60000 elements
Select a group: Select a group: ^MReading frame 0 time 0.000 ^MReading frame 0 time 200000.000
Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.2#

Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.2#
[irene1022:52095:0] Caught signal 11 (Segmentation fault) ==== backtrace ====
2 0x0000000000068d1c mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:641
3 0x000000000006926c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:616
4 0x0000000000035270 killpg() ??:0
5 0x00000000000471ad _IO_vfprintf_internal() :0
6 0x0000000000051827 __GI_fprintf() :0
7 0x00000000003b3cd8 xvgr_header() ??:0
8 0x00000000003b3c70 xvgropen_type() ??:0
9 0x0000000000545400 dist_plot.a() gmx_mindist.c:0
10 0x0000000000543990 gmx_mindist() ??:0
11 0x00000000001e1ff3 _ZN3gmx24Comman

With GMX2018 and 2018.2 (fatal error) ----------------------

Group 0 (Protein_HeavyAtoms) has 4976 elements
Group 1 (OGNG_AlkylChain) has 1530 elements
Group 2 ( OGNG_Headgroup) has 2244 elements
Group 3 (OGNG_All_HeavyAtoms) has 3774 elements
Group 4 ( Water_oxygen) has 60000 elements
Select a group: Select a group: ^MReading frame 0 time 0.000 ^MReading frame 0 time 200000.000
Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_min_res.xvg.1#

Back Off! I just backed up 3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg to ./#3FHH_102OGNG_complex_CHARMM36_TIP3P_Protein_AlkylChain_Contact_Number.xvg.1#

-------------------------------------------------------
Program: gmx mindist, version 2018
Source file: src/gromacs/fileio/gmxfio.cpp (line 345)

Fatal error:
Cannot open file with NULL filename string

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
+ echo 0 2
+ echo 0 3
+ echo 0 4
+ exit 0

Please note that if I remove the "-group" and "-printresname" arguments the program also crashes

And other possible bug in the tool is that you add -printresname, no output files contains the residue names (tested with GMX4.6.7)

Thank you

#2 Updated by Gerrit Code Review Bot about 1 year ago

Gerrit received a related patchset '1' for Issue #2653.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~I26ccc7df37e5cc6a0276ecce50036aba452e0a45
Gerrit URL: https://gerrit.gromacs.org/8439

#3 Updated by Paul Bauer about 1 year ago

Hello, the issue here is that mindist expects to get all the output files defined at least with the default filename.
I added a check that makes sure the program complains about missing the output file in this case.

#4 Updated by Paul Bauer about 1 year ago

  • Status changed from New to Resolved

#5 Updated by Stéphane Abel about 1 year ago

Paul Bauer wrote:

Applied in changeset 034183c82d46d45981ef9543a77c80193b3f72ac.

OK Paul by adding the missing file name (here with the -od with the "mindist.xvg") it works for all the gromacs versions I have. Thanks

#6 Updated by Paul Bauer about 1 year ago

  • Status changed from Resolved to Closed

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