[MITgcm-support] error while writing pickup files with Cray compilers

Tue Apr 11 16:39:36 EDT 2017

Hi Jody,

yes, it does start writing the pickup file.
I also made a few other tests (of course much shorter than 100 y!), and I got always the same error. Also, the configuration works with the gnu compiler, but if the Cray compiler is really 10x faster it would be nice to use it!

I wonder if the pickup file is overwritten or if it is appending to the file...? Maybe it is doing something funny when trying to appending to it?

Thanks,
Laura

________________________________
From: Jody Klymak [jklymak at uvic.ca]
Sent: 11 April 2017 21:27
To: mitgcm-support at mitgcm.org
Subject: Re: [MITgcm-support] error while writing pickup files with Cray compilers

Hi Laura,

Are you sure the mitgcm can write to the directory it is trying to write to?  Does it *start* to write the pickup file?

These are just dumb questions.  Maybe it truly is a compiler issue, but it seems more likely it is a configuration issue.   Obviously, for testing I’d suggest writing a pickup file well before 100 y has passed.

Good luck,

Jody

On 11 Apr 2017, at  11:21 AM, Laura Cimoli <laura.cimoli at physics.ox.ac.uk<mailto:laura.cimoli at physics.ox.ac.uk>> wrote:

Hello Jody,

sorry I forgot to mention that all my other outputs are in netcdf format, and they look fine.
The data file is attached.

Thanks,
Laura

________________________________
From: Jody Klymak [jklymak at uvic.ca<mailto:jklymak at uvic.ca>]
Sent: 11 April 2017 19:01
To: mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] error while writing pickup files with Cray compilers

Are you able to write any mds files?  i.e. did the T.000000000000.data file write?  Can you supply your `data` file?

Cheers,   Jody

On 11 Apr 2017, at  10:54 AM, Laura Cimoli <laura.cimoli at physics.ox.ac.uk<mailto:laura.cimoli at physics.ox.ac.uk>> wrote:

Hello,

this question is relevant mainly for Archer user, but of course any help is appreciated!

I have recently tried to use Cray instead of gnu compilers, since the model should run much faster according to what stated here<http://www.archer.ac.uk/community/eCSE/eCSE03-09/eCSE03-09_White_Paper.pdf>. I have to admit I have not read that report in detail, but I hope that there are not particular constraints on the use of Cray compilers on Archer.

I used the linux_ia64_cray_archer optfile, as indicated in the report.

At a first glance, the model is compiled without any odd warning, and seems to run without any problem, but it crashes when writing the pickup file. This is the message I got (the whole error file is attached):

lib-5058 : UNRECOVERABLE library error
A read system call read less data than expected.

Encountered during a direct access unformatted WRITE to unit 9
Fortran unit 9 is connected to a direct unformatted unblocked file:
"pickup.0001752000.data"

_pmiu_daemon(SIGCHLD): [NID 02940] [c7-1c0s15n0] [Tue Apr 11 08:49:37 2017] PE RANK 69 exit signal Aborted
[NID 02940] 2017-04-11 08:49:37 Apid 26123498: initiated application termination

I am writing the permanent pickup file, and I don't have any temporary pickup file.

The only weird warning I have noticed in the genmake.log file (attached) is below, but I don't know whether it is related to the problem reported above:

running: check_HAVE_SIGREG()
cc -c genmake_tc_1.c
CC-513 craycc: WARNING File = genmake_tc_1.c, Line = 22
A value of type "void *" cannot be assigned to an entity of type
"void (*)(int, siginfo_t *, void *)".
s.sa_sigaction = (void *)killhandler;
^
Total warnings detected in genmake_tc_1.c: 1
program hello
integer anint
common /iv/ anint
external sigreg
call sigreg(anint)
end
ftn -o genmake_tc genmake_tc_2.f genmake_tc_1.o
--> set HAVE_SIGREG='t'

Does anyone know why the Cray compilers return this error while writing the output binary file?

Many thanks,
Laura
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--
Jody Klymak
http://web.uvic.ca/~jklymak/

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Jody Klymak
http://web.uvic.ca/~jklymak/

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