Hello,
I'm trying to converge a Hartree Fock computation, but I keep running into a Segmentation fault error. I've attached the quantum espresso output files from the input that I used, as well as the failed yambo run. I've tried with a few different yambo compilations, playing with the linear algebra versions as indicated in this post viewtopic.php?t=1834, but the error remained the same.
I hadn't been getting this error before, with any BSE or GW calculations, but in this run I increased ecutwfc in my quantum espresso input. Presumably it's some sort of memory issue, but I've watched the nodes running the calculation and they never go anywhere near their memory limit (they don't even reach 1/5 the total ram on the node). My guess is that there's some sort of bug in how OpenMP is used, but I'm interested in your opinion. I'm using yambo-5.1.1
Thanks,
Miles
Segmentation fault (core dumped) in HF calculation
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Segmentation fault (core dumped) in HF calculation
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Miles Johnson
California Institute of Technology
PhD candidate in Applied Physics
California Institute of Technology
PhD candidate in Applied Physics
- Daniele Varsano
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Re: Segmentation fault (core dumped) in HF calculation
Dear Miles,
can you please attach also the log files of your run?
Best,
Daniele
can you please attach also the log files of your run?
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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- Posts: 30
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Re: Segmentation fault (core dumped) in HF calculation
Attached, for one of the compilations it also has the line:
but for the most part the log files just say segmentation fault
Code: Select all
*** stack smashing detected ***: <unknown> terminated
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Miles Johnson
California Institute of Technology
PhD candidate in Applied Physics
California Institute of Technology
PhD candidate in Applied Physics
- Daniele Varsano
- Posts: 3844
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: Segmentation fault (core dumped) in HF calculation
Dear Miles,
is this one of the log files contained in the LOG directory? It seems pretty much the batch script output.
I would like to have a look to the yambo log files to understand in which part of the run it crashes.
Best,
Daniele
is this one of the log files contained in the LOG directory? It seems pretty much the batch script output.
I would like to have a look to the yambo log files to understand in which part of the run it crashes.
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
-
- Posts: 30
- Joined: Thu Jan 26, 2023 9:27 pm
Re: Segmentation fault (core dumped) in HF calculation
My mistake, attached below.
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Miles Johnson
California Institute of Technology
PhD candidate in Applied Physics
California Institute of Technology
PhD candidate in Applied Physics
- Daniele Varsano
- Posts: 3844
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: Segmentation fault (core dumped) in HF calculation
Dear Miles,
not totally clear what's happening, but it could be a memory issue.
Can you try to run using more CPUs (if you have them available) defining in input a parallelization scheme allowing memory distribution among cores:
where #ncpu us the total number of cores you are using.
Best,
Daniele
not totally clear what's happening, but it could be a memory issue.
Can you try to run using more CPUs (if you have them available) defining in input a parallelization scheme allowing memory distribution among cores:
Code: Select all
SE_CPU= " 1 1 #ncpu" # [PARALLEL] CPUs for each role
SE_ROLEs= "q qp b"
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/