Dear Amber Users,
Hope you had a great holiday! I recently built the MPI version of Amber20, but I did not find MMPBSA.py.MPI under the amber20 bin folder as well. I checked the cmake.log file and there was no error for mpi4py. The mpi4py is on my Amber.conda list. How can I compile the MMPBSA.py.MPI in this case? I’m attaching the cmake.log file. Thank you!
Best wishes,
Haoxi
On Dec 12, 2020, at 7:56 PM, Setyanto Md <stwahyudi.md.gmail.com<mailto:stwahyudi.md.gmail.com>> wrote:
[External Email]
Hi Elvis,
Thanks for the suggestion,
It works for me.
Setyanto Tri W
-------
Biophysics Division,
Department of Physics - Bogor Agricultural University
Gedung Fisika Wing-S Lt.2 Jl. Meranti
Kampus IPB Darmaga
Bogor - 16680
Indonesia
On Sat, Dec 12, 2020 at 8:40 PM Elvis Martis <elvis_bcp.elvismartis.in<mailto:elvis_bcp.elvismartis.in>>
wrote:
Hi
With legacy build, I had a similar experience.
A workaround for this is, after you compiled serial version install mpi4py
using amber.conda install mpi4py. After this compile the mpi version.
However, I am not sure if this will solve the cmake build.
On Saturday, December 12, 2020, Setyanto Md <
stwahyudi.md.gmail.com<mailto:
stwahyudi.md.gmail.com>>
wrote:
Dear Amber User and Developer.
I've been successful to compile Amber20 using cmake.
I just followed the instruction in this site:
https://urldefense.proofpoint.com/v2/url?u=https-3A__ambermd.org_pmwiki_index.php_Main_CMake-2DQuick-2DStart&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SSRyv2p8U1S1O1OKefEt8WnSpJO5RS47PLTtN6Y14jU&m=w_ZA5Lsou5J15RAigem4tnIBLKcksf2dle54xtWMBWY&s=A6ohx47G9ZMGcSF-EH5SJjJAoBBjfNfLUVeGI0_UqGs&e=
1. Choose a build directory outside of the Amber source directory
2. Run the configuration command.
This is the command that I used:
cmake ../amber20_src/
-DCMAKE_INSTALL_PREFIX=/home/coto/software/amber20-build-gnu
-DCOMPILER=GNU -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=FALSE
-DPYTHON_EXECUTABLE=/usr/bin/python
I also managed to build pmemd.cuda using advice from Professor David. A
Case.
but unfortunately, the MMPBSA.py.MPI not successful compile.
I'll try to called in command line : MMPBSA.py.MPI, was not appear.
I've used mpich and configure it in folder AmberTools/sr.
I also try to re-compile using legacy configure, and the result is the
same.
can anyone help? Thank you
My computer configuration:
OS : Ubuntu 20
CPU : AMD threadripper 3970x
GPU: Nvidia RTX3080
Setyanto Tri W
-------
Biophysics Division,
Department of Physics - IPB Univesity
Gedung Fisika Wing-S Lt.2 Jl. Meranti
Kampus IPB Darmaga
Bogor - 16680
Indonesia
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SSRyv2p8U1S1O1OKefEt8WnSpJO5RS47PLTtN6Y14jU&m=w_ZA5Lsou5J15RAigem4tnIBLKcksf2dle54xtWMBWY&s=k4eOub7gu-aE5aj71g2WxPPTmG8GutSp9qv-lfS85CU&e=
--
Best Regards
Elvis
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:
AMBER.ambermd.org>
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SSRyv2p8U1S1O1OKefEt8WnSpJO5RS47PLTtN6Y14jU&m=w_ZA5Lsou5J15RAigem4tnIBLKcksf2dle54xtWMBWY&s=k4eOub7gu-aE5aj71g2WxPPTmG8GutSp9qv-lfS85CU&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:
AMBER.ambermd.org>
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SSRyv2p8U1S1O1OKefEt8WnSpJO5RS47PLTtN6Y14jU&m=w_ZA5Lsou5J15RAigem4tnIBLKcksf2dle54xtWMBWY&s=k4eOub7gu-aE5aj71g2WxPPTmG8GutSp9qv-lfS85CU&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: cmake.log
Received on Mon Jan 04 2021 - 09:30:03 PST
