p2y error

Come here to discuss issues with using the p2y converter from PWscf to Yambo, how to best run PWscf , link with the IOTK library, and so on.

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hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

p2y error

Post by hammouri » Fri Mar 25, 2022 3:07 am

Hi all,
I came across this error which I do not know how to resolve.

./p2y: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory


I tried this command: ldconfig -p | grep gfortran, and this is what I got: libgfortran.so.3 (libc6,x86-64) => /lib64/libgfortran.so.3

I checked the version of Fortran:
GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

I am running my calculations on a HTCondor, so I may need to ask them to update the shared library.

Any ideas on how to work around this problem?
---------------------------------------------------------------
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

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Daniele Varsano
Posts: 3893
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: p2y error

Post by Daniele Varsano » Fri Mar 25, 2022 8:39 am

Dear Hammouri,

if you are running in a cluster, be sure you are loading the same module of compiler you used to compile the code before running the executable.
if p2y look for that libs it means they were used when compiling the code.

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/

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hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: p2y error

Post by hammouri » Fri Mar 25, 2022 5:13 pm

Oh yes I forgot to load the module I used before.
I am trying to run it on the queue so I created two files:
submit file:
## Submit file options for running your program
executable =run_script
log = job.log
output = job.out
error = job.err

# arguments = (if you want to pass any to the shell script)
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
transfer_input_files =p2y, wfc$(ProcId).dat,data-file-schema.xml, charge-density.dat,Ag.UPF, F.UPF, Zn.UPF
requirements = (HasChtcSoftware == true)
request_cpus = 1
request_memory = 8GB
request_disk = 2GB

queue 1

and run_script:
#!/bin/bash

# Commands to enable modules, and then load an appropriate MP/MPI module
export PATH
. /etc/profile.d/modules.sh
module load OpenMPI/3.1.4-GCC-8.3.0
mpirun -np 1 ./p2y
~


but it does not work as if I run it on the head node. In fact I got this error when I ran the two files:
Error in routine p2y_init (1):
QE format not recognised/compatible (was wf_collect set to true?)

I do not want to run it on the head node to avoid any issues issues with the cluster.
Maybe the two files above need to be changed so p2y can be run without any issue.


---------------------------------------------------------------
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
Daniele Varsano
Posts: 3893
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: p2y error

Post by Daniele Varsano » Tue Mar 29, 2022 9:20 pm

Dear Hammouri,

p2y it is just a converter and the run last less than a minute.
You can run it in interactive mode.
Once you realized it works, you can try to run in the queue inspecting what went wrong in your script.

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/

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: p2y error

Post by hammouri » Wed Mar 30, 2022 3:30 am

I decided to run it on the head node since it does not take long time.

Thank you, Daniele!
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

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