search

Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
Other
261 stars 59 forks source link

Problem with HTMD update #951

Closed musabbirsaeed closed 4 years ago

musabbirsaeed commented 4 years ago

Hello, After updating HTMD, the program is not running anymore. As I write "from htmd.ui import *" in jupyter, the message I am getting is

" AttributeError: module 'numpy' has no attribute 'block' "

Later I installed fresh HTMD and i am getting the same message.

stefdoerr commented 4 years ago

Hi, sorry for this. We are updating now the new installation instructions because we had to upgrade to numpy 1.17. You can install HTMD in a new conda environment

conda create -n my_environment_name
conda activate my_environment_name
conda install htmd=1.19 -c acellera -c psi4 -c conda-forge
musabbirsaeed commented 4 years ago

Hi, HTMD problem is solved. Even I updated to htmd1.21.0. But the problem is Equilibration() is not running properly. The message I am getting:

2020-02-02 00:13:26,851 - jobqueues.localqueue - INFO - Trying to determine all GPU devices 2020-02-02 00:13:26,904 - jobqueues.localqueue - INFO - Using GPU devices 0 2020-02-02 00:13:26,906 - jobqueues.localqueue - INFO - Trying to determine all GPU devices 2020-02-02 00:13:26,943 - jobqueues.localqueue - INFO - Queueing /home/saeed/equil 2020-02-02 00:13:26,945 - jobqueues.localqueue - INFO - Running /home/saeed/equil on device 0 2020-02-02 00:13:27,631 - jobqueues.localqueue - ERROR - Error in simulation /home/saeed/equil. Command '/home/saeed/equil/job.sh' returned non-zero exit status 1.

Can you please help me out. Thanks

stefdoerr commented 4 years ago

Try running /home/saeed/equil/run.sh from a command line and see what error it gives you. Also in the folder /home/saeed/equil/ there should already be a file called log.txt which will say what error there was.

musabbirsaeed commented 4 years ago

After changing the GPU driver equilibrium is running. But later production is not running. It is saying "acemd: command not found" Later I run the run.sh file with ACEMD3. and got the message "ERROR: /home/user/conda/conda-bld/acemd3_1573499276231/work/src/mdsim/input.cpp line 192: Unknown input keyword "acemd" "

I have edited the run.sh file from "acemd" to "acemd3" then i got "ERROR: /home/user/conda/conda-bld/acemd3_1573499276231/work/src/mdsim/input.cpp line 192: Unknown input keyword "acemd3" "

stefdoerr commented 4 years ago

can you show me your "input" file? there seems to be some wrong command in there . ACEMD should not be reading the run.sh file.

On Sun, Feb 2, 2020 at 10:54 PM MASaeed44 notifications@github.com wrote:

After changing the GPU driver equilibrium is running. But later production is not running. It is saying "acemd: command not found" Later I run the run.sh file with ACEMD3. and got the message "ERROR: /home/user/conda/conda-bld/acemd3_1573499276231/work/src/mdsim/input.cpp line 192: Unknown input keyword "acemd" "

I have edited the run.sh file from "acemd" to "acemd3" then i got "ERROR: /home/user/conda/conda-bld/acemd3_1573499276231/work/src/mdsim/input.cpp line 192: Unknown input keyword "acemd3" "

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Acellera/htmd/issues/951?email_source=notifications&email_token=AB4RLAUIXWPLSL2U7YEZWKTRA4XJ3A5CNFSM4KLZ72XKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKSAXVA#issuecomment-581176276, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4RLASTGGHQI7GSLXJUQA3RA4XJ3ANCNFSM4KLZ72XA .

musabbirsaeed commented 4 years ago

The problem is solved now. I was using "htmd.protocols.production_v4". "htmd.protocols.production_v6" solved everything. Thank you.

stefdoerr commented 4 years ago

Great :)