Open CarmenSheppard opened 2 years ago
This is always a tricky one. Potentially we've got a memory related bug, these sometimes cause a crash and sometimes don't. First, it would be helpful to get a minimal example.
files.txt
and see if you get the same issue?poppunk_sketch
to a) create the sketch database and b) create the distance matrix work? Both with the full set, and the smaller set of ten.Depending on those results, I will hopefully be able to rerun with the same settings, and look at a memory debugger.
Hi John,
Yes same issue with --create-db running 10 or 2 files.
However --sketch seemed to work fine with 3000ish files (I stopped it manually as I was limited to 1 thread and it was going to take a while!).
also worked fine to completion with 10 files. as did --query DB with 10 files. I think it would have been fine with the larger dataset too but I am currently unable to get more than 1 thread node due to congestion on the hpc!
So it seems specific to the --create-db command.
Carmen
From: John Lees @.> Sent: 10 November 2021 12:09 To: johnlees/PopPUNK @.> Cc: Carmen Sheppard @.>; Author @.> Subject: Re: [johnlees/PopPUNK] Help with issues running poppunk in HPC environment (Issue #193)
This is always a tricky one. Potentially we've got a memory related bug, these sometimes cause a crash and sometimes don't. First, it would be helpful to get a minimal example.
Depending on those results, I will hopefully be able to rerun with the same settings, and look at a memory debugger.
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Ok that's useful. Would it be possible to share those two files? If not, I'll see if I can reproduce in a debugger with two test files of my own.
Ok I'll email you the assemblies directly. It doesnt' seem to matter which files I try though I've attempted to run different datasets with the same issues.
Hi Carmen,
I've tried to reproduce this bug, but I am unable to. I've also run through with valgrind (which lets you check for segfaults) and that doesn't turn anything up during the call to sketching made by --create-db
.
You should at least see:
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
(with backend: sketchlib v1.7.4
sketchlib: /home/jlees/miniconda3/envs/pp-clean/lib/python3.9/site-packages/pp_sketchlib.cpython-39-x86_64-linux-gnu.so)
or similar when the code runs. I think any error before that is due to one of the dependencies.
I have a vague memory of there being some possible issues with the graph-tool
package. Could you try:
1) Cloning this repository
2) Within that clone, run pushd PopPUNK && for i in $(ls *.py); do sed -i -e 's/import graph_tool/#import graph_tool/' $i; done && popd
which will comment out all the graph_tool imports
3) Run your command from before, but using python poppunk-runner.py
in place of poppunk
If that prints some output, but then eventually fails on graph_tool being missing, then that's the culprit.
Hi John,.
Yes looks like the graph tool is the problem :
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
(with backend: sketchlib v1.7.4
sketchlib: /home/carmen.sheppard/.conda/envs/poppunk/lib/python3.9/site-packages/pp_sketchlib.cpython-39-x86_64-linux-gnu.so)
Traceback (most recent call last):
File "/home/carmen.sheppard/software/PopPUNK/poppunk-runner.py", line 10, in <module>
main()
File "/hpscol02/tenant2/hpc_storage/home/carmen.sheppard/software/PopPUNK/PopPUNK/__main__.py", line 293, in main
setGtThreads(args.threads)
File "/hpscol02/tenant2/hpc_storage/home/carmen.sheppard/software/PopPUNK/PopPUNK/utils.py", line 37, in setGtThreads
if gt.openmp_enabled():
NameError: name 'gt' is not defined
Is there a previous fix for this issue?
Ok, glad that we seem to have nailed it down. Unfortunately I don't write or support graph tool so the help I can provide is more limited, but some suggestions I have:
1) Raise an issue on the graph tool gitlab: https://git.skewed.de/count0/graph-tool/-/issues
I would recommend, if you can, running the failing command under valgrind
to help them understand. For example:
valgrind --leak-check=full --track-origins=yes --error-limit=no poppunk --create-db --output poppunk/poppunk_db --r-files rfile.txt --threads 1 2> pp_valgrind.txt
and then uploading pp_valgrind.txt
with the issue report and your conda environment list. (you'll of course want to do this with the code where gt was still being imported)
2) Try installing a different/older version of graph-tool from conda. You can specify the version for example with conda install graph-tool==2.4.2
. If this works, it would be helpful to post an issue on the conda recipe noting the issue.
3) Follow the instructions to build from source: https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions#manual-compilation Again, if this works it would be helpful to post an issue on the conda recipe page
Ok I tried versions of graph-tool in conda back to 2.35 with the same fault. The earliest version in conda-forge 2.29 then caused other incompatibilities so I didn't try that.
We'll think about the other suggestions you made. Thanks very much for your help!
@nickjcroucher asked me to raise a formal issue when I mentioned to him
*Versions**
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Command used and output returned
poppunk --create-db --output poppunk/poppunk_db --r-files files.txt --threads 1 Segmentation fault (core dumped)
Describe the bug
I cannot run poppunk --create-db on the hpc environment. after a few seconds it reports a segmentation fault (core dumped) and does not give any other output. Other commands can successfully run. I have deleted and recreated the poppunk environment on the cluster and tried starting afresh. I can run poppunk fine on my laptop. I have checked versions of the hpc software against the same software on my from conda env list and then manually installed any versions that were different but this didnt' change the error, now everything that is on my laptop poppunk env is the same as the hpc poppunk env..
The hpc is running an older version of conda which I cannot update 4.9.2 (laptop 4.10.3) I'm wondering if there's something the --create-db calls that causes the issue on the hpc?