Question: Is AWS Pcluster supported by SCHISM? about schism

[zeekus]

seem to get a similar error when I run this on our controller node without mpiexec.

[centos@ip-10-137-0-172 tune44h]$ /modeling/pschism/icm_Balg/build/bin/pschism_ICM_ANALYSIS_PREC_EVAP_TVD-VL

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x2B815BBEC6D7
#1 0x2B815BBECD1E
#2 0x2B815C89B3FF
#3 0x53C5D0 in calkwq_
#4 0x554151 in ecosystem_
#5 0x45F1EC in schism_step_
#6 0x404C4B in schism_main_
#7 0x404CB6 in MAIN__ at schism_driver.F90:?
Segmentation fault (core dumped)

[zeekus]

It appears pschism will work on AWS pcluster if Intel Ifortan and Intel MPI libraries are used. I am thinking that this code may not be compatible with Gfortran. Has anyone successfully run pschism on Gfortran ? To get things to compile on our end I had to modify two files. Maybe there are other Gfortran compatiblity issues I am missing.

Files and lines modified:

1. File: ./icm_Balg/src/Hydro/schism_init.F90:5451.114
2. File: ./icm_Balg/src/ICM/icm_sed_flux.F90

Ref: ./icm_Balg/src/Hydro/schism_init.F90:5451.114
Summary: array format issue. All strings need to be the same size for gfortran to compile.

','CPOC ','tlfveg ','tstveg ','trtveg ','hcanveg','lfsav ','stsav ','rts

Error: Different CHARACTER lengths (7/6) in array constructor at (1)
make[3]: *** [Hydro/CMakeFiles/hydro.dir/schism_init.F90.o] Error 1
make[2]: *** [Hydro/CMakeFiles/hydro.dir/all] Error 2
make[1]: *** [Driver/CMakeFiles/pschism.dir/rule] Error 2

Ref: ./icm_Balg/src/ICM/read_icm_input.F90:326:
Summary: Gfortan seems to process '/*' as a closing comment in line 326.

Output:
/modeling/pschism/icm_Balg/src/ICM/read_icm_input.F90:326:0: warning: extra tokens at end of #endif directive [enabled by default]
#endif ICM_PH
^
/modeling/pschism/icm_Balg/src/ICM/icm_sed_flux.F90:1385:0: error: unterminated comment
!with all state variables in unit of g/*, no need to transfer
^
Error: Unexpected end of file in '/modeling/pschism/icm_Balg/src/ICM/icm_sed_flux.F90'
make[3]: *** [ICM/CMakeFiles/icm.dir/icm_sed_flux.F90.o] Error 1
make[3]: *** Waiting for unfinished jobs....

[josephzhang8]

Hi Teddy: Many of us have used gcc. The error you mentioned below seems to be from an older tag (5.7.0?) and has been fixed in newer tag v5.10.0.

…

-Joseph Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466 From: Teddy Knab ***@***.***> Sent: Thursday, September 29, 2022 8:10 AM To: schism-dev/schism ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [schism-dev/schism] Question: Is AWS Pcluster supported by SCHISM? (Issue #88) [EXTERNAL to VIMS received message] Per an email from NOAA who runs this on AWS it appears pschism will work on AWS pcluster if Intel Ifortan and Intel MPI libraries are used. I am thinking that this code may not be compatible with Gfortran. Has anyone successfully run pschism on Gfortran ? To get things to compile on our end I had to modify two files. Maybe there are other compatiblity issues I am missing. Files and lines modified: 1. File: ./icm_Balg/src/Hydro/schism_init.F90:5451.114 2. File: ./icm_Balg/src/ICM/icm_sed_flux.F90 Ref: ./icm_Balg/src/Hydro/schism_init.F90:5451.114 Summary: array format issue. All strings need to be the same size for gfortran to compile. ','CPOC ','tlfveg ','tstveg ','trtveg ','hcanveg','lfsav ','stsav ','rts Error: Different CHARACTER lengths (7/6) in array constructor at (1) make[3]: *** [Hydro/CMakeFiles/hydro.dir/schism_init.F90.o] Error 1 make[2]: *** [Hydro/CMakeFiles/hydro.dir/all] Error 2 make[1]: *** [Driver/CMakeFiles/pschism.dir/rule] Error 2 Ref: ./icm_Balg/src/ICM/read_icm_input.F90:326: Summary: Gfortan seems to process '/*' as a closing comment in line 326. Output: /modeling/pschism/icm_Balg/src/ICM/read_icm_input.F90:326:0: warning: extra tokens at end of #endif directive [enabled by default] #endif ICM_PH ^ /modeling/pschism/icm_Balg/src/ICM/icm_sed_flux.F90:1385:0: error: unterminated comment !with all state variables in unit of g/*, no need to transfer ^ Error: Unexpected end of file in '/modeling/pschism/icm_Balg/src/ICM/icm_sed_flux.F90' make[3]: *** [ICM/CMakeFiles/icm.dir/icm_sed_flux.F90.o] Error 1 make[3]: *** Waiting for unfinished jobs.... - Reply to this email directly, view it on GitHub<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F88%23issuecomment-1262186601&data=05%7C01%7Cyjzhang%40vims.edu%7Cc67dcdb6b0ac492491d108daa2137a64%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638000501781978945%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HvLBB594lGh60Pr7w7fQ7eh%2FNx2g8B9Ika0YYTd8vYk%3D&reserved=0>, or unsubscribe<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ6DKG6ANEFK5EOZ3MLWAWBIBANCNFSM6AAAAAAQWYNOLM&data=05%7C01%7Cyjzhang%40vims.edu%7Cc67dcdb6b0ac492491d108daa2137a64%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638000501781978945%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=s%2BJyXZSTvbQTxxB5wdHL%2F3usuBywpxQXDOdpMKMkFXo%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>

[josephzhang8]

Since ICM is very important for EPA/CBPO, v5.10.0 is the one to use. Zhengui has spent a lot of time cleaning up ICM for the past year.

…

-Joseph Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466 From: Y. Joseph Zhang Sent: Thursday, September 29, 2022 9:08 AM To: schism-dev/schism ***@***.***>; schism-dev/schism ***@***.***> Cc: Subscribed ***@***.***> Subject: RE: [schism-dev/schism] Question: Is AWS Pcluster supported by SCHISM? (Issue #88) Hi Teddy: Many of us have used gcc. The error you mentioned below seems to be from an older tag (5.7.0?) and has been fixed in newer tag v5.10.0.

-Joseph Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466 From: Teddy Knab ***@***.******@***.***>> Sent: Thursday, September 29, 2022 8:10 AM To: schism-dev/schism ***@***.******@***.***>> Cc: Subscribed ***@***.******@***.***>> Subject: Re: [schism-dev/schism] Question: Is AWS Pcluster supported by SCHISM? (Issue #88) [EXTERNAL to VIMS received message] Per an email from NOAA who runs this on AWS it appears pschism will work on AWS pcluster if Intel Ifortan and Intel MPI libraries are used. I am thinking that this code may not be compatible with Gfortran. Has anyone successfully run pschism on Gfortran ? To get things to compile on our end I had to modify two files. Maybe there are other compatiblity issues I am missing. Files and lines modified: 1. File: ./icm_Balg/src/Hydro/schism_init.F90:5451.114 2. File: ./icm_Balg/src/ICM/icm_sed_flux.F90 Ref: ./icm_Balg/src/Hydro/schism_init.F90:5451.114 Summary: array format issue. All strings need to be the same size for gfortran to compile. ','CPOC ','tlfveg ','tstveg ','trtveg ','hcanveg','lfsav ','stsav ','rts Error: Different CHARACTER lengths (7/6) in array constructor at (1) make[3]: *** [Hydro/CMakeFiles/hydro.dir/schism_init.F90.o] Error 1 make[2]: *** [Hydro/CMakeFiles/hydro.dir/all] Error 2 make[1]: *** [Driver/CMakeFiles/pschism.dir/rule] Error 2 Ref: ./icm_Balg/src/ICM/read_icm_input.F90:326: Summary: Gfortan seems to process '/*' as a closing comment in line 326. Output: /modeling/pschism/icm_Balg/src/ICM/read_icm_input.F90:326:0: warning: extra tokens at end of #endif directive [enabled by default] #endif ICM_PH ^ /modeling/pschism/icm_Balg/src/ICM/icm_sed_flux.F90:1385:0: error: unterminated comment !with all state variables in unit of g/*, no need to transfer ^ Error: Unexpected end of file in '/modeling/pschism/icm_Balg/src/ICM/icm_sed_flux.F90' make[3]: *** [ICM/CMakeFiles/icm.dir/icm_sed_flux.F90.o] Error 1 make[3]: *** Waiting for unfinished jobs.... - Reply to this email directly, view it on GitHub<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism%2Fissues%2F88%23issuecomment-1262186601&data=05%7C01%7Cyjzhang%40vims.edu%7Cc67dcdb6b0ac492491d108daa2137a64%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638000501781978945%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HvLBB594lGh60Pr7w7fQ7eh%2FNx2g8B9Ika0YYTd8vYk%3D&reserved=0>, or unsubscribe<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFBKNZ6DKG6ANEFK5EOZ3MLWAWBIBANCNFSM6AAAAAAQWYNOLM&data=05%7C01%7Cyjzhang%40vims.edu%7Cc67dcdb6b0ac492491d108daa2137a64%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638000501781978945%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=s%2BJyXZSTvbQTxxB5wdHL%2F3usuBywpxQXDOdpMKMkFXo%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>

[zeekus]

Thanks. It seems I was using the wrong version.

#version pulled
[centos@ip-10-137-0-172 tune44h]$ /modeling/pschism/icm_Balg/build/bin/pschism_ICM_ANALYSIS_PREC_EVAP_TVD-VL -version

schism v5.9.0mod
git hash 2e289ae (20 commits since semantic tag, edits=False)

#version 5.10
[centos@ip-10-137-0-172 tune44h]$ /modeling/pschism/icm_Balg_v5.10/build/bin/pschism_ICM_ANALYSIS_PREC_EVAP_TVD-VL -version

schism develop
git hash aaa98b3

The proper version seems to be running.

[centos@ip-10-137-0-172 tune44h]$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
248 compute pschism_ centos R 19:13 8 compute-dy-slurmworkers-[1-8]

ifort (IFORT) 2021.6.0 20220226
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