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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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No license found for ACEMD3 #1012

Closed aqred2 closed 3 years ago

aqred2 commented 3 years ago

I tried to install acemd3 following the docs several times: 

$ conda create -n acemd_env -c conda-forge -c acellera acemd3
$ conda activate acemd_env

And then tried to run it and the license could not be found. The issue goes as follows:

#
# ACEMD version 3.3.0
#
# Copyright (C) 2017-2019 Acellera (www.acellera.com)
#
# When publishing, please cite:
#   ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
#   M. J. Harvey, G. Giupponi and G. De Fabritiis,
#   J Chem. Theory. Comput. 2009 5(6), pp1632-1639
#   DOI: 10.1021/ct9000685
#
# Arguments:
#   input: input
#   platform: 
#   device: 
#   ncpus: 
#   precision: mixed
#
# Looking for node-locked license in [/opt/acellera/license.dat] 
# Looking for node-locked license in [/opt/acellera/.acellera/license.dat] 
# Looking for node-locked license in [/opt/acellera/.htmd/license.dat] 
# Looking for node-locked license in [/agh/home/aqred/license.dat] 
# Looking for node-locked license in [/agh/home/aqred/.acellera/license.dat] 
# Looking for node-locked license in [/agh/home/aqred/.htmd/license.dat] 
#
# ACEMD has expired!
# Download an update from https://www.acellera.com or with 'conda update acemd3'.
#

I could not find a license.dat file on my computer. Where should it be installed? Any help is appreciated.

thanks

raimis commented 3 years ago

If you want a licence, you have to buy it. More details: https://software.acellera.com/docs/latest/acemd/licence.html

aqred2 commented 3 years ago

I would like to run it on the basic mode. Device 0, no support. But running acemd3 input searches automatically for the license.

stefdoerr commented 3 years ago

You can ignore the license errors. The real error is that this version of ACEMD has expired because it's old. I'm not sure why it's pulling 3.3.0 instead of 3.5.0.

stefdoerr commented 3 years ago

@aqred2 try installing 3.5.0 directly with conda install acemd3=3.5.0 -c acellera -c conda-forge I have the impression it might be an issue with cudatoolkit versions. Can you post here the CUDA version that the nvidia-smi command gives you?

aqred2 commented 3 years ago 
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 465.19.01    Driver Version: 465.19.01    CUDA Version: 11.3     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  NVIDIA GeForce ...  Off  | 00000000:01:00.0  On |                  N/A |
| 36%   37C    P8    N/A /  N/A |    447MiB /  1993MiB |      7%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   1  NVIDIA Quadro P400  Off  | 00000000:02:00.0 Off |                  N/A |
| 34%   37C    P8    N/A /  N/A |      4MiB /  2000MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
aqred2 commented 3 years ago

Apparently I run on compatability issues. Anything I can try from my side?: 

aqred@hjk:/projects/aqred/KR5$ conda create -n acemd_env -c conda-forge -c acellera acemd3=3.5.0
Collecting package metadata (repodata.json): done
Solving environment: | 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                         

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package fftw conflicts for:
acemd3=3.5.0 -> fftw[version='>=3.3,<3.4.0a0']
Package boost-cpp conflicts for:
acemd3=3.5.0 -> boost-cpp[version='>=1.74,<1.75.0a0']
Package plumed conflicts for:
acemd3=3.5.0 -> plumed[version='>=2.7,<2.8.0a0']
Package ocl-icd conflicts for:
acemd3=3.5.0 -> ocl-icd[version='>=2.3.0,<3.0a0']
Package cudatoolkit conflicts for:
acemd3=3.5.0 -> cudatoolkit[version='>=10.1,<10.2.0a0|>=10.2,<10.3.0a0|>=11.2,<11.3.0a0']
Package libstdcxx-ng conflicts for:
acemd3=3.5.0 -> libstdcxx-ng[version='>=9.3.0']
Package libgcc-ng conflicts for:
acemd3=3.5.0 -> libgcc-ng[version='>=9.3.0']
Package ocl-icd-system conflicts for:
acemd3=3.5.0 -> ocl-icd-system[version='>=1.0,<1.1.0a0']
Package __glibc conflicts for:
acemd3=3.5.0 -> __glibc[version='>=2.17,<3.0.a0']
raimis commented 3 years ago

Try this:

conda create -n acemd_env -c conda-forge -c acellera acemd3=3.5 cudatoolkit=11.2
aqred2 commented 3 years ago

Got this.

Collecting package metadata (repodata.json): done
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                         

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package libgcc-ng conflicts for:
acemd3=3.5 -> libgcc-ng[version='>=9.3.0']
cudatoolkit=11.2 -> libgcc-ng[version='>=9.3.0|>=9.4.0']
Package ocl-icd-system conflicts for:
acemd3=3.5 -> ocl-icd-system[version='>=1.0,<1.1.0a0']
Package boost-cpp conflicts for:
acemd3=3.5 -> boost-cpp[version='>=1.74,<1.75.0a0']
Package cudatoolkit conflicts for:
acemd3=3.5 -> cudatoolkit[version='>=10.1,<10.2.0a0|>=10.2,<10.3.0a0|>=11.2,<11.3.0a0']
Package libstdcxx-ng conflicts for:
cudatoolkit=11.2 -> libstdcxx-ng[version='>=9.3.0|>=9.4.0']
acemd3=3.5 -> libstdcxx-ng[version='>=9.3.0']
Package plumed conflicts for:
acemd3=3.5 -> plumed[version='>=2.7,<2.8.0a0']
Package __glibc conflicts for:
acemd3=3.5 -> __glibc[version='>=2.17,<3.0.a0']
cudatoolkit=11.2 -> __glibc[version='>=2.17,<3.0.a0']
Package ocl-icd conflicts for:
acemd3=3.5 -> ocl-icd[version='>=2.3.0,<3.0a0']
Package fftw conflicts for:
acemd3=3.5 -> fftw[version='>=3.3,<3.4.0a0']The following specifications were found to be incompatible with your CUDA driver:

  - cudatoolkit=11.2 -> __cuda[version='>=11.2.2|>=11.2|>=11.2.1']

Your installed CUDA driver is: 11.3

This didn't work either: conda create -n acemd_env -c conda-forge -c acellera acemd3=3.5 cudatoolkit=11.3

raimis commented 3 years ago

Don't change the version of cudatoolkit.

aqred2 commented 3 years ago

As I wrote, I only tried it after this command did not work.

conda create -n acemd_env -c conda-forge -c acellera acemd3=3.5 cudatoolkit=11.2

raimis commented 3 years ago

What is your version of conda?

aqred2 commented 3 years ago

conda 4.7.11 Let me know if i should upgrade it.

raimis commented 3 years ago

Yes, upgrade.

aqred2 commented 3 years ago

Updating conda worked. Thanks