Hello Michael,
Could you share how did you install the cuda.parallel version? I have been keep getting the MPI unfound error from cmake. I'm also using Rocky 8.10. Thanks in advance!
Regards,
Nil
On 7/11/24, 10:33 AM, "Michael Shokhen via AMBER" <amber.ambermd.org <mailto:amber.ambermd.org>> wrote:
Dear AMBER experts,
I have installed on my server Amber24 and AmberTools24.
All four tests were completed without errors: test.serial, test.parallel, tcsh shell. test.cuda.serial, test.cuda.parallel.
I have on my sever Rocky Linux VERSION="8.10 (Green Obsidian)"; tcsh shell.
Unfortunately, I received an error report when running pdb4amber command. See copy from terminal below.
I need your advice how to resolve the problem.
Thank you,
Michael
/var/spool/scratch/shokhen/US4_Gln391_Gly_Gly_Ser627
> pdb4amber -i US4_Gly_Gly_nh.pdb -o US4_Gly_Gly_reduced.amber.pdb --dry –reduce
==================================================
Summary of pdb4amber for: –reduce
===================================================
Traceback (most recent call last):
File "/var/spool/scratch/shokhen/amber24/bin/pdb4amber", line 33, in <module>
sys.exit(load_entry_point('pdb4amber==22.0', 'console_scripts', 'pdb4amber')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/pdb4amber/pdb4amber.py", line 819, in main
run(
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/pdb4amber/pdb4amber.py", line 516, in run
parm = parmed.read_PDB(pdbin)
^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/parmed/formats/pdb.py", line 422, in parse
fileobj = genopen(filename, 'r')
^^^^^^^^^^^^^^^^^^^^^^
File "/var/spool/scratch/shokhen/amber24/lib/python3.11/site-packages/parmed/utils/io.py", line 95, in genopen
return open(name, mode, encoding=DEFAULT_ENCODING)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '–reduce'
>
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Received on Thu Jul 11 2024 - 11:00:02 PDT
