segmentation fault occurred

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wenjian
segmentation fault occurred

Hi everyone,

I complied Py-ChemShell v20 and it was done successfully. I tried to run a test of single point calculation which was interfaced with ORCA 4.1. It crashed with errors:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libifcoremt.so.5 00002B739F33B627 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002B73A10005D0 Unknown Unknown Unknown
libifcoremt.so.5 00002B739F33B2D2 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002B73A10005D0 Unknown Unknown Unknown

The same test was checked with the v19.0.4 of Py-ChemShell, which was compiled with the same settings. It was finished without any problem. May you help me with this issue. It fails at the start, but I want to continue other tests.

Thank you.

ylu
ylu's picture
Hi Wenjian,

Hi Wenjian,

you could run the shell script "run_validation.tcsh" in folder "tests" to see if other tests work, by commands such as:
./run_validation.tcsh chemsh fragment
./run_validation.tcsh chemsh cluster

Then we can figure out the GULP problem together.

Thank you very much.

Kind regards,

You

wenjian
Hi You,

Hi You,

Thanks a lot for your suggestions. I have tried to run the script. I attached the output related to the v20 below.

[user21@login09 tests]$ ./run_validation.tcsh chemsh cluster
Testing executable: /public/home/user21/software/chemsh-py-20.0.1/tests/../bin/intel/chemsh
File cluster/bulk_coordination_scaled_cart.py -------- FAILED --------- F libpthread-2.17.s 00002ACC88CDE5D0 Unknown Unknown Unknown 0.118
File cluster/bulk_coordination_scaled_frac.py -------- FAILED --------- F libpthread-2.17.s 00002AF0A4DC05D0 Unknown Unknown Unknown 0.106
File cluster/bulk_molecular.py -------- FAILED --------- F libpthread-2.17.s 00002B12858675D0 Unknown Unknown Unknown 0.105
File cluster/bulk_valence_matrix.py -------- FAILED --------- F libpthread-2.17.s 00002B31EDAE35D0 Unknown Unknown Unknown 0.102
File cluster/bulk_partition_implicit.py -------- FAILED --------- F libpthread-2.17.s 00002B68F10735D0 Unknown Unknown Unknown 0.093
File cluster/bulk_partition_explicit.py -------- FAILED --------- F libpthread-2.17.s 00002B6D4E60F5D0 Unknown Unknown Unknown 0.092
File cluster/surface_coordination_scaled.py -------- FAILED --------- F libpthread-2.17.s 00002B986F8ED5D0 Unknown Unknown Unknown 0.128
File cluster/surface_partition_implicit.py -------- FAILED --------- F libpthread-2.17.s 00002B90B37FA5D0 Unknown Unknown Unknown 0.105
File cluster/surface_partition_explicit.py -------- FAILED --------- F libpthread-2.17.s 00002AB1E6BAB5D0 Unknown Unknown Unknown 0.113
F cluster bulk_coordination_scaled_cart.py 0.118 libpthread-2.17.s 00002ACC88CDE5D0 Unknown Unknown Unknown
F cluster bulk_coordination_scaled_frac.py 0.106 libpthread-2.17.s 00002AF0A4DC05D0 Unknown Unknown Unknown
F cluster bulk_molecular.py 0.105 libpthread-2.17.s 00002B12858675D0 Unknown Unknown Unknown
F cluster bulk_valence_matrix.py 0.102 libpthread-2.17.s 00002B31EDAE35D0 Unknown Unknown Unknown
F cluster bulk_partition_implicit.py 0.093 libpthread-2.17.s 00002B68F10735D0 Unknown Unknown Unknown
F cluster bulk_partition_explicit.py 0.092 libpthread-2.17.s 00002B6D4E60F5D0 Unknown Unknown Unknown
F cluster surface_coordination_scaled.py 0.128 libpthread-2.17.s 00002B986F8ED5D0 Unknown Unknown Unknown
F cluster surface_partition_implicit.py 0.105 libpthread-2.17.s 00002B90B37FA5D0 Unknown Unknown Unknown
F cluster surface_partition_explicit.py 0.113 libpthread-2.17.s 00002AB1E6BAB5D0 Unknown Unknown Unknown
Failures: 9 Passes: 0 Unsupported: 0 Unknown: 0
[user21@login09 tests]$ ./run_validation.tcsh chemsh fragment
Testing executable: /public/home/user21/software/chemsh-py-20.0.1/tests/../bin/intel/chemsh
File fragment/connect_ethane.py -------- FAILED --------- F libpthread-2.17.s 00002B6B723735D0 Unknown Unknown Unknown 0.099
File fragment/connect_urea.py -------- FAILED --------- F libpthread-2.17.s 00002B394BFBC5D0 Unknown Unknown Unknown 0.091
File fragment/connect_quartz.py -------- FAILED --------- F libpthread-2.17.s 00002AB942B3C5D0 Unknown Unknown Unknown 0.112
File fragment/connect_mgo.py -------- FAILED --------- F libpthread-2.17.s 00002AC0B94295D0 Unknown Unknown Unknown 0.124
File fragment/connect_mgo_shells.py -------- FAILED --------- F libpthread-2.17.s 00002AF6B0E245D0 Unknown Unknown Unknown 0.079
File fragment/connect_options.py -------- FAILED --------- F libpthread-2.17.s 00002AFD519865D0 Unknown Unknown Unknown 0.081
File fragment/save_json_ethane.py -------- FAILED --------- F libpthread-2.17.s 00002AE61A34C5D0 Unknown Unknown Unknown 0.099
File fragment/save_json_mgo.py -------- FAILED --------- F libpthread-2.17.s 00002B2F19EB45D0 Unknown Unknown Unknown 0.105
File fragment/save_json_mgo_shells.py -------- FAILED --------- F libpthread-2.17.s 00002B4AD7FD55D0 Unknown Unknown Unknown 0.095
File fragment/save_punch_ethane.py -------- FAILED --------- F libpthread-2.17.s 00002B3649BC15D0 Unknown Unknown Unknown 0.099
File fragment/save_punch_mgo.py -------- FAILED --------- F libpthread-2.17.s 00002AF9D428F5D0 Unknown Unknown Unknown 0.106
File fragment/save_punch_mgo_shells.py -------- FAILED --------- F libpthread-2.17.s 00002B72A35425D0 Unknown Unknown Unknown 0.101
F fragment connect_ethane.py 0.099 libpthread-2.17.s 00002B6B723735D0 Unknown Unknown Unknown
F fragment connect_urea.py 0.091 libpthread-2.17.s 00002B394BFBC5D0 Unknown Unknown Unknown
F fragment connect_quartz.py 0.112 libpthread-2.17.s 00002AB942B3C5D0 Unknown Unknown Unknown
F fragment connect_mgo.py 0.124 libpthread-2.17.s 00002AC0B94295D0 Unknown Unknown Unknown
F fragment connect_mgo_shells.py 0.079 libpthread-2.17.s 00002AF6B0E245D0 Unknown Unknown Unknown
F fragment connect_options.py 0.081 libpthread-2.17.s 00002AFD519865D0 Unknown Unknown Unknown
F fragment save_json_ethane.py 0.099 libpthread-2.17.s 00002AE61A34C5D0 Unknown Unknown Unknown
F fragment save_json_mgo.py 0.105 libpthread-2.17.s 00002B2F19EB45D0 Unknown Unknown Unknown
F fragment save_json_mgo_shells.py 0.095 libpthread-2.17.s 00002B4AD7FD55D0 Unknown Unknown Unknown
F fragment save_punch_ethane.py 0.099 libpthread-2.17.s 00002B3649BC15D0 Unknown Unknown Unknown
F fragment save_punch_mgo.py 0.106 libpthread-2.17.s 00002AF9D428F5D0 Unknown Unknown Unknown
F fragment save_punch_mgo_shells.py 0.101 libpthread-2.17.s 00002B72A35425D0 Unknown Unknown Unknown
Failures: 12 Passes: 0 Unsupported: 0 Unknown: 0

However, I have tried the v19.0 also and it can work very well. I think there used to be an issue about compiling the new version, but I have no clue where it could be. Thanks a lot for your help.

[user21@login09 tests]$ ./run_validation.tcsh chemsh cluster
Testing executable: /public/home/user21/software/chemsh-py-19.0.4/tests/../bin/intel/chemsh
File cluster/bulk_coordination_scaled_cart.py P OK 89.174
File cluster/bulk_coordination_scaled_frac.py P OK 82.105
File cluster/bulk_molecular.py P OK 191.120
File cluster/bulk_valence_matrix.py P OK 95.878
P cluster bulk_coordination_scaled_cart.py 89.174 OK
P cluster bulk_coordination_scaled_frac.py 82.105 OK
P cluster bulk_molecular.py 191.120 OK
P cluster bulk_valence_matrix.py 95.878 OK
Failures: 0 Passes: 4 Unsupported: 0 Unknown: 0
[user21@login09 tests]$ ./run_validation.tcsh chemsh fragment
Testing executable: /public/home/user21/software/chemsh-py-19.0.4/tests/../bin/intel/chemsh
File fragment/connect_ethane.py P OK 0.645
File fragment/connect_urea.py P OK 0.659
File fragment/connect_quartz.py P OK 0.653
File fragment/connect_mgo.py P OK 0.669
File fragment/connect_mgo_shells.py P OK 0.707
File fragment/save_json_ethane.py P OK 0.732
File fragment/save_json_mgo.py P OK 0.745
File fragment/save_json_mgo_shells.py P OK 0.650
File fragment/save_punch_ethane.py P OK 0.677
File fragment/save_punch_mgo.py P OK 0.654
File fragment/save_punch_mgo_shells.py P OK 0.681
P fragment connect_ethane.py 0.645 OK
P fragment connect_urea.py 0.659 OK
P fragment connect_quartz.py 0.653 OK
P fragment connect_mgo.py 0.669 OK
P fragment connect_mgo_shells.py 0.707 OK
P fragment save_json_ethane.py 0.732 OK
P fragment save_json_mgo.py 0.745 OK
P fragment save_json_mgo_shells.py 0.650 OK
P fragment save_punch_ethane.py 0.677 OK
P fragment save_punch_mgo.py 0.654 OK
P fragment save_punch_mgo_shells.py 0.681 OK
Failures: 0 Passes: 11 Unsupported: 0 Unknown: 0

Best regards,

Wenjian

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