Molcas Forum

qling

Member

Registered: 2021-04-12

Posts: 4

[SOLVED] Molcas Environment Setup

How to set the environment variable (MOLCAS) and Molcas driver (molcas)
export MOLCAS=/home/molcas/molcas.version
export PATH=$PATH:$HOME/bin

I followed the above step of Qiuckstart guide, and then run molcas xxx.input. It shows that "-bash: molcas: command not found".

What is the problem?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: [SOLVED] Molcas Environment Setup

If you're using OpenMolcas, you should use "pymolcas" instead of "molcas", and you should copy it somewhere in you path (e.g. in $HOME/bin). See https://gitlab.com/Molcas/OpenMolcas/-/ … stallation

qling

Member

Registered: 2021-04-12

Posts: 4

Re: [SOLVED] Molcas Environment Setup

Thanks. I am using Openmolcas and I can run molcas on my loading node now. However, I cannot submit the task to the queue by script.

The script is given as following:

#!/bin/sh
export PATH=$PATH:$HOME/molcas-build
export MOLCAS_NPROCS=2
bsub -q test -o %J.log -e %J.err python ~/molcas-build/pymolcas sew.input > sew.output

And the ouput is given:

/home/phys/ckduan2/molcas-build/bin/seward.exe: error while loading shared libraries: libhdf5.so.8: cannot open shared object file: No such file or directory
/home/phys/ckduan2/molcas-build/bin/seward.exe: error while loading shared libraries: libhdf5.so.8: cannot open shared object file: No such file or directory
cannot open file for reading: No such file or directory
0 parnell_reduce: cannot open source file rc.local
cannot open file for reading: No such file or directory
1 parnell_reduce: cannot open source file rc.local
0 parnell: ABORTING
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[cli_0]: readline failed
1 parnell: ABORTING
Abort(1) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
Traceback (most recent call last):
  File "/home/phys/ckduan2/molcas-build/pymolcas", line 587, in <module>
    sys.exit(main(os.path.realpath(f)))
  File "<string>", line 217, in main
  File "<string>", line 776, in auto
  File "<string>", line 198, in run
  File "<string>", line 346, in run
  File "<string>", line 842, in run_module
  File "<string>", line 1328, in run
  File "<string>", line 1198, in _read_rc
  File "<string>", line 75, in utf8_open
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/sew/rc.global'

Can you give me some guidance, please? Thank you!

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: [SOLVED] Molcas Environment Setup

That is something the technical support of your HPC should help you with. Typically, though, your script should have something like:

#!/bin/sh
export PATH=$PATH:$HOME/molcas-build
export MOLCAS_NPROCS=2
~/molcas-build/pymolcas sew.input > sew.output

and then you submit the script with "bsub name_of_the_script". The specific error you're getting is about missing HDF5 libraries, you probably need to load the corresponding module inside the script too.

qling

Member

Registered: 2021-04-12

Posts: 4

Re: [SOLVED] Molcas Environment Setup

I can successfully run the program now, thanks!