[MITgcm-support] [EXTERNAL] Re: MITgcm-support Digest, Vol 237, Issue 1
Menemenlis, Dimitris (US 329B)
dimitris.menemenlis at jpl.nasa.gov
Sat Mar 4 09:10:39 EST 2023
Perhaps try compiling without optimization to see if issue remains?
On Mar 3, 2023, at 4:15 PM, mario wrk <wrkmario at gmail.com> wrote:
Thanks for pointing that out! the scratch files point to data.exch2 and data.ctrl I excluded some pkg one by one, but I still have some similar issues,
in the end, there is a segmentation fault, srun: error: l10551: task 256: Segmentation fault, now I highly suspect it might be some compiler issues, cuz it was good with some verification examples, but my own configuration substantially increased resolution and I wanted to compile/run in multi-processors
I also noticed there were similar discussions before: http://mailman.mitgcm.org/pipermail/mitgcm-support/2018-June/011593.html<https://urldefense.us/v3/__http://mailman.mitgcm.org/pipermail/mitgcm-support/2018-June/011593.html__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKaxKv-vC$>
Best,
Mario
255: forrtl: severe (28): CLOSE error, unit 11, file "Unknown"
255: Image PC Routine Line Source
255: libifcoremt.so.5 00001555553EFBDE for__exit_handler Unknown Unknown
255: libifcoremt.so.5 00001555553FC78E for__signal_handl Unknown Unknown
255: libpthread-2.28.s 0000155550C3BC20 Unknown Unknown Unknown
255: libc-2.28.so<https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKTl0Fk4g$> 000015555095316B unlink Unknown Unknown
255: libifcoremt.so.5 00001555553E18B1 for__close_proc Unknown Unknown
255: libifcoremt.so.5 00001555553E0EB0 for_close Unknown Unknown
255: mitgcmuv_ad 0000000000902A3F Unknown Unknown Unknown
255: mitgcmuv_ad 00000000009E2F4A Unknown Unknown Unknown
255: mitgcmuv_ad 00000000009DB0E5 Unknown Unknown Unknown
255: mitgcmuv_ad 00000000009F7D38 Unknown Unknown Unknown
255: mitgcmuv_ad 000000000097DDEA Unknown Unknown Unknown
714: mitgcmuv_ad 0000000000403852 Unknown Unknown Unknown
714: libc-2.28.so<https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKTl0Fk4g$> 0000155550887493 __libc_start_main Unknown Unknown
714: mitgcmuv_ad 000000000040375E Unknown Unknown Unknown
255: mitgcmuv_ad 0000000000403852 Unknown Unknown Unknown
255: libc-2.28.so<https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKTl0Fk4g$> 0000155550887493 __libc_start_main Unknown Unknown
255: mitgcmuv_ad 000000000040375E Unknown Unknown Unknown
1481: forrtl: error (78): process killed (SIGTERM)
1481: Image PC Routine Line Source
1481: libifcoremt.so.5 00001555553FC76C for__signal_handl Unknown Unknown
1481: libpthread-2.28.s 0000155550C3BC20 Unknown Unknown Unknown
1481: libpthread-2.28.s 0000155550C3B1D6 __open64 Unknown Unknown
1481: libifcoremt.so.5 00001555554911B1 for__open_proc Unknown Unknown
1481: libifcoremt.so.5 000015555540CCBE for_open Unknown Unknown
1481: mitgcmuv_ad 000000000097F1F5 Unknown Unknown Unknown
1481: mitgcmuv_ad 000000000090122F Unknown Unknown Unknown
1481: mitgcmuv_ad 00000000009E2F4A Unknown Unknown Unknown
1481: mitgcmuv_ad 00000000009DB0E5 Unknown Unknown Unknown
1481: mitgcmuv_ad 00000000009F7D38 Unknown Unknown Unknown
1481: mitgcmuv_ad 000000000097DDEA Unknown Unknown Unknown
On Fri, Mar 3, 2023 at 6:35 PM <mitgcm-support-request at mitgcm.org<mailto:mitgcm-support-request at mitgcm.org>> wrote:
Send MITgcm-support mailing list submissions to
mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>
To subscribe or unsubscribe via the World Wide Web, visit
http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support<https://urldefense.us/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKcuWvN_K$>
or, via email, send a message with subject or body 'help' to
mitgcm-support-request at mitgcm.org<mailto:mitgcm-support-request at mitgcm.org>
You can reach the person managing the list at
mitgcm-support-owner at mitgcm.org<mailto:mitgcm-support-owner at mitgcm.org>
When replying, please edit your Subject line so it is more specific
than "Re: Contents of MITgcm-support digest..."
Today's Topics:
1. too many values for NAMELIST variable (mario wrk)
2. Re: too many values for NAMELIST variable
(Menemenlis, Dimitris (US 329B))
3. Re: too many values for NAMELIST variable
(Carroll, Dustin (US 329C-Affiliate))
----------------------------------------------------------------------
Message: 1
Date: Fri, 3 Mar 2023 17:48:03 +0300
From: mario wrk <wrkmario at gmail.com<mailto:wrkmario at gmail.com>>
To: mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>
Subject: [MITgcm-support] too many values for NAMELIST variable
Message-ID:
<CAAfDP0dnjOKcAO682mC1+z1BDGmAYXdOaC3-iLQfJa0E8kinjA at mail.gmail.com<mailto:CAAfDP0dnjOKcAO682mC1%2Bz1BDGmAYXdOaC3-iLQfJa0E8kinjA at mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"
Dear MITgcm community,
I was running a high resolution model in parallel with OpenMPI and got the
error below.
Does anyone have a clue?
Best,
Mario
799: forrtl: severe (18): too many values for NAMELIST variable, unit 11,
file .........run_ad/scratch1.000000799, line 3315, position 7
799: Image PC Routine Line
Source
799: libifcoremt.so.5 00001555553E6E79 for__io_return Unknown
Unknown
799: libifcoremt.so.5 000015555542F3F5 for_read_seq_nml Unknown
Unknown
799: mitgcmuv_ad 0000000000786AC8 Unknown Unknown
Unknown
799: mitgcmuv_ad 000000000077F9A4 Unknown Unknown
Unknown
799: mitgcmuv_ad 0000000000862732 Unknown Unknown
Unknown
799: mitgcmuv_ad 00000000008BD780 Unknown Unknown
Unknown
799: mitgcmuv_ad 00000000004037C2 Unknown Unknown
Unknown
799: libc-2.28.so<https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKTl0Fk4g$> 0000155550887493 __libc_start_main Unknown
Unknown
799: mitgcmuv_ad 00000000004036CE Unknown Unknown
Unknown
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230303/14bbf386/attachment-0001.html<https://urldefense.us/v3/__http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230303/14bbf386/attachment-0001.html__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKbgSCSBw$>>
------------------------------
Message: 2
Date: Fri, 3 Mar 2023 15:11:44 +0000
From: "Menemenlis, Dimitris (US 329B)"
<dimitris.menemenlis at jpl.nasa.gov<mailto:dimitris.menemenlis at jpl.nasa.gov>>
To: MITgcm Support <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
Subject: Re: [MITgcm-support] too many values for NAMELIST variable
Message-ID: <541236B8-2F43-46B3-A2BE-67CC43AD6D94 at jpl.nasa.gov<mailto:541236B8-2F43-46B3-A2BE-67CC43AD6D94 at jpl.nasa.gov>>
Content-Type: text/plain; charset="us-ascii"
There is a problem with one of your runtime parameter files (data or data.*) in your runtime directory run_ad.
On Mar 3, 2023, at 6:48 AM, mario wrk <wrkmario at gmail.com<mailto:wrkmario at gmail.com>> wrote:
Dear MITgcm community,
I was running a high resolution model in parallel with OpenMPI and got the error below.
Does anyone have a clue?
Best,
Mario
799: forrtl: severe (18): too many values for NAMELIST variable, unit 11, file .........run_ad/scratch1.000000799, line 3315, position 7
799: Image PC Routine Line Source
799: libifcoremt.so.5 00001555553E6E79 for__io_return Unknown Unknown
799: libifcoremt.so.5 000015555542F3F5 for_read_seq_nml Unknown Unknown
799: mitgcmuv_ad 0000000000786AC8 Unknown Unknown Unknown
799: mitgcmuv_ad 000000000077F9A4 Unknown Unknown Unknown
799: mitgcmuv_ad 0000000000862732 Unknown Unknown Unknown
799: mitgcmuv_ad 00000000008BD780 Unknown Unknown Unknown
799: mitgcmuv_ad 00000000004037C2 Unknown Unknown Unknown
799: libc-2.28.so<https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKTl0Fk4g$><https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!M2W-DPfuY1q_PomytTcSW2ZHGL19dSVErDKaeBk6O3OIi_YZzV1x60iLZjKuaNrKDqjCzquEc3Kh4E8hzb2sHWWSPPDd$> 0000155550887493 __libc_start_main Unknown Unknown
799: mitgcmuv_ad 00000000004036CE Unknown Unknown Unknown
_______________________________________________
MITgcm-support mailing list
MITgcm-support at mitgcm.org<mailto:MITgcm-support at mitgcm.org>
https://urldefense.us/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!M2W-DPfuY1q_PomytTcSW2ZHGL19dSVErDKaeBk6O3OIi_YZzV1x60iLZjKuaNrKDqjCzquEc3Kh4E8hzb2sHXBtL2F1$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230303/3f126b2a/attachment-0001.html<https://urldefense.us/v3/__http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230303/3f126b2a/attachment-0001.html__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKaUh3sgz$>>
------------------------------
Message: 3
Date: Fri, 3 Mar 2023 15:35:12 +0000
From: "Carroll, Dustin (US 329C-Affiliate)"
<dustin.carroll at jpl.nasa.gov<mailto:dustin.carroll at jpl.nasa.gov>>
To: "mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>" <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
Subject: Re: [MITgcm-support] too many values for NAMELIST variable
Message-ID:
<SJ0PR09MB90307EB60388A8CD177F8130BDB39 at SJ0PR09MB9030.namprd09.prod.outlook.com<mailto:SJ0PR09MB90307EB60388A8CD177F8130BDB39 at SJ0PR09MB9030.namprd09.prod.outlook.com>>
Content-Type: text/plain; charset="windows-1252"
To follow up on Dimitris? comment, if you open the file ?scratch1.000000799? in your run_ad directory
and look at line 3315, position 7 this will tell you where the syntax error / incorrect parameter value
occurred in your data.* file.
From: MITgcm-support <mitgcm-support-bounces at mitgcm.org<mailto:mitgcm-support-bounces at mitgcm.org>> on behalf of Menemenlis, Dimitris (US 329B) <dimitris.menemenlis at jpl.nasa.gov<mailto:dimitris.menemenlis at jpl.nasa.gov>>
Date: Friday, March 3, 2023 at 7:12 AM
To: MITgcm Support <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
Subject: [EXTERNAL] Re: [MITgcm-support] too many values for NAMELIST variable
There is a problem with one of your runtime parameter files (data or data.*) in your runtime directory run_ad.
On Mar 3, 2023, at 6:48 AM, mario wrk <wrkmario at gmail.com<mailto:wrkmario at gmail.com>> wrote:
Dear MITgcm community,
I was running a high resolution model in parallel with OpenMPI and got the error below.
Does anyone have a clue?
Best,
Mario
799: forrtl: severe (18): too many values for NAMELIST variable, unit 11, file .........run_ad/scratch1.000000799, line 3315, position 7
799: Image PC Routine Line Source
799: libifcoremt.so.5 00001555553E6E79 for__io_return Unknown Unknown
799: libifcoremt.so.5 000015555542F3F5 for_read_seq_nml Unknown Unknown
799: mitgcmuv_ad 0000000000786AC8 Unknown Unknown Unknown
799: mitgcmuv_ad 000000000077F9A4 Unknown Unknown Unknown
799: mitgcmuv_ad 0000000000862732 Unknown Unknown Unknown
799: mitgcmuv_ad 00000000008BD780 Unknown Unknown Unknown
799: mitgcmuv_ad 00000000004037C2 Unknown Unknown Unknown
799: libc-2.28.so<https://urldefense.us/v3/__http://libc-2.28.so__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKTl0Fk4g$><https://urldefense.us/v3/__http:/libc-2.28.so__;!!PvBDto6Hs4WbVuu7!M2W-DPfuY1q_PomytTcSW2ZHGL19dSVErDKaeBk6O3OIi_YZzV1x60iLZjKuaNrKDqjCzquEc3Kh4E8hzb2sHWWSPPDd$> 0000155550887493 __libc_start_main Unknown Unknown
799: mitgcmuv_ad 00000000004036CE Unknown Unknown Unknown
_______________________________________________
MITgcm-support mailing list
MITgcm-support at mitgcm.org<mailto:MITgcm-support at mitgcm.org>
https://urldefense.us/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!M2W-DPfuY1q_PomytTcSW2ZHGL19dSVErDKaeBk6O3OIi_YZzV1x60iLZjKuaNrKDqjCzquEc3Kh4E8hzb2sHXBtL2F1$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230303/c74ea89b/attachment.html<https://urldefense.us/v3/__http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230303/c74ea89b/attachment.html__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKRYdfUND$>>
------------------------------
Subject: Digest Footer
_______________________________________________
MITgcm-support mailing list
MITgcm-support at mitgcm.org<mailto:MITgcm-support at mitgcm.org>
http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support<https://urldefense.us/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKcuWvN_K$>
------------------------------
End of MITgcm-support Digest, Vol 237, Issue 1
**********************************************
_______________________________________________
MITgcm-support mailing list
MITgcm-support at mitgcm.org
https://urldefense.us/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!PvBDto6Hs4WbVuu7!PW3tsJze90OC9AZksTklqll_4rOFJ960_dMKKzN_IrfuD8n7DhhAJcHxS3Bjhzsf3W94H-e37L-aZ7MEptTBKcuWvN_K$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20230304/7e96aed9/attachment-0001.html>
More information about the MITgcm-support
mailing list