ASTRAL Test Failure

[LilithMary]

Hi Benoit,

I hope you are well.

I'm a part-time Informatician at Leicester University trying to set up ParGenes on a Linux server for biology students to use and I've encountered some issues during installation.

After multiple tries each failing for a reason, I finally got everything installed and executed the run_tests.py code. Even though it passed the first 5 tests successfully, it failed on the sixth one (i.e. ASTRAL).

Would you please have a look at the report attached and help me solve the problem?

Kind regards, Maryam

report.txt

[BenoitMorel]

Dear Maryam,

Thanks for the report. Are you trying to install via bionconda or from the github repository? If you install with bioconda, are you trying to run run_test.py "manually" or was it run by the package installer?

In both cases, can you try this: cd /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/ && ./checker.sh

and if it works, run the following: rm -rf /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc && /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/pargenes/pargenes-hpc.py -a /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/smalldata/fasta_files -o /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc -r /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/smalldata/raxml_global_options.txt -c 4 -s 3 -p 3 --scheduler split

and copy-paste the logs from the console. This is the command called by the test script that fails, but I need the output printed in the console, because it might contain more logs than the pargenes_log.txt file or the report file.

Kind regards, Benoit

[LilithMary]

Dear Benoit,

Many thanks for your prompt response.

I've tried to install via bioconda as well as directly via githup repository but both have caused issues. I ran checker.sh and run_tests.py code manually afterwards.

I just tried the first command you suggested and this is the output:

(pargenes_env_3) @.*** ~]$ cd /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/ && ./checker.sh Running checker.sh... ERROR: pargenes/pargenes_binaries/raxml-ng-mpi.so does not exist

This is the content of pargenes_binaries directory:

(pargenes_env_3) @. ParGenes]$ cd pargenes/pargenes_binaries/ (pargenes_env_3) @. pargenes_binaries]$ ls astral.jar lib modeltest-ng mpi-scheduler raxml-ng

Is raxml-ng the same as raxml-ng-mpi.so which it says is missing? I'd very much appreciate your help with this and I look forward to hearing from you.

Kind regards, Maryam

On Wed, May 26, 2021 at 3:38 PM BenoitMorel @.***> wrote:

Dear Maryam,

Thanks for the report. Are you trying to install via bionconda or from the github repository? If you install with bioconda, are you trying to run run_test.py "manually" or was it run by the package installer?

In both cases, can you try this: cd /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/ && ./checker.sh

and if it works, run the following: rm -rf /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc && /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/pargenes/pargenes-hpc.py -a /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/smalldata/fasta_files -o /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc -r /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/smalldata/raxml_global_options.txt -c 4 -s 3 -p 3 --scheduler split

and copy-paste the logs from the console. This is the command called by the test script that fails, but I need the output printed in the console, because it might contain more logs than the pargenes_log.txt file or the report file.

Kind regards, Benoit

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/ParGenes/issues/69#issuecomment-848824844, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQLXMLN2WVGGRRREIJDI6VLTPUBXBANCNFSM45SB4SZQ .

[BenoitMorel]

Dear Maryam,

raxml-ng-mpi.so is not built when MPI is not installed or can't be found. This does not result in an error in the installation process, but it makes the -hpc tests fail. If you can't install MPI, users can still use ParGenes, but ParGenes won't be able to parallelize over distributed memory nodes (see also https://github.com/BenoitMorel/ParGenes/wiki/Parallelization)

However, it shouldn't be an issue when installing with conda, because MPI should be in the list of dependencies...

Let me know if this helps Benoit

Le jeu. 27 mai 2021 à 10:32, LilithMary @.***> a écrit :

Dear Benoit,

Many thanks for your prompt response.

I've tried to install via bioconda as well as directly via githup repository but both have caused issues. I ran checker.sh and run_tests.py code manually afterwards.

I just tried the first command you suggested and this is the output:

(pargenes_env_3) @.*** ~]$ cd /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/ && ./checker.sh Running checker.sh... ERROR: pargenes/pargenes_binaries/raxml-ng-mpi.so does not exist

This is the content of pargenes_binaries directory:

(pargenes_env_3) @. ParGenes]$ cd pargenes/pargenes_binaries/ (pargenes_env_3) @. pargenes_binaries]$ ls astral.jar lib modeltest-ng mpi-scheduler raxml-ng

Is raxml-ng the same as raxml-ng-mpi.so which it says is missing? I'd very much appreciate your help with this and I look forward to hearing from you.

Kind regards, Maryam

On Wed, May 26, 2021 at 3:38 PM BenoitMorel @.***> wrote:

Dear Maryam,

Thanks for the report. Are you trying to install via bionconda or from the github repository? If you install with bioconda, are you trying to run run_test.py "manually" or was it run by the package installer?

In both cases, can you try this: cd /lustre/alice3/data/evassvis/software/anaconda3/ParGenes/ && ./checker.sh

and if it works, run the following: rm -rf

/lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc &&

/lustre/alice3/data/evassvis/software/anaconda3/ParGenes/pargenes/pargenes-hpc.py -a

/lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/smalldata/fasta_files -o

/lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc -r

/lustre/alice3/data/evassvis/software/anaconda3/ParGenes/tests/smalldata/raxml_global_options.txt -c 4 -s 3 -p 3 --scheduler split

and copy-paste the logs from the console. This is the command called by the test script that fails, but I need the output printed in the console, because it might contain more logs than the pargenes_log.txt file or the report file.

Kind regards, Benoit

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/BenoitMorel/ParGenes/issues/69#issuecomment-848824844>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AQLXMLN2WVGGRRREIJDI6VLTPUBXBANCNFSM45SB4SZQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/ParGenes/issues/69#issuecomment-849446573, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UPMGQTPKJRN7NHVEETTPX7TJANCNFSM45SB4SZQ .

[LilithMary]

Dear Benoit,

Thank you very much for your helpful response!

I installed MPI (using conda) and then ParGenes from GitHub (tried installing ParGenes with conda as well, it said there are conflicting dependencies, I assume with MPI since it was a fresh environment otherwise) and it passed all the tests successfully.

I very much appreciate your help in setting this up and I'll get in touch again if any further issues arise in working with ParGenes.

Kind regards, Maryam

[BenoitMorel]

Dear Maryam,

Thank you for your feedback. I am glad that it worked. Don't hesitate to get in touch if you encounter any further issue.

Best, Benoit