gmindist (GMX5.14, 2018 vesrions) crashes with segmentation fault - Redmine #2653
Archive from user: Stéphane Abel
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
(from redmine: issue id 2653, created on 2018-09-26 by gmxdefault, closed on 2018-10-04)
- Changesets:
- Revision 034183c8 by Paul Bauer on 2018-09-27T14:37:13Z:
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