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Merge pull request #14 from KaihangShi/main
Update Installation instructions
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‎Cluster-Setup/NERSC/readme.md‎

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## Installation instructions on [NERSC](https://www.nersc.gov/)
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## Follow this instruction to install gRASPA-DP on the NERSC Perlmutter cluster.
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# SPECIAL NOTE:
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* If you don't need the DeepPotential, download the code, `cd src_clean/`, and start from [step 6](#Step-6).
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* If you don't need the ML potential, download the code, `cd src_clean/`, and start from [step 6](#Step-6).
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* Installation on other clusters are similar to on Perlmutter of NERSC. Follow the instructions here, and if you encounter issues, please consult with your institution's IT.
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* [Northwestern Quest IT](https://www.it.northwestern.edu/departments/it-services-support/research/computing/quest/)
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* cppflow-patch is for the LCLin model, you can do ```mv cppflow-patch LCLin``` when patching the code with LCLin's ML potential
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* Similarly, do ```mv libtorch-patch Allegro``` for using the Allegro ML potential
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* Check the [nvhpc](https://developer.nvidia.com/hpc-sdk) version. Currently the code works for **22.5 and 22.7**
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* on NERSC, you can do ```module load nvhpc/22.7``` to use the 22.7 version of nvhpc.
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* Also check out the [issue on this topic](https://github.com/snurr-group/gRASPA/issues/9)
@@ -42,14 +40,15 @@ wget https://download.pytorch.org/libtorch/cu117/libtorch-cxx11-abi-shared-with-
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unzip libtorch-cxx11-abi-shared-with-deps-2.0.1+cu117.zip
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```
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# Step 5
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Modify line 64 in `patch.py` file to `patch_model=['Allegro']`. Then,
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Modify line 65 in `patch.py` file to `patch_model=['Allegro']`. Then,
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```shellscript
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python patch.py
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```
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Now the patched source code is in `patch_libtorch_Allegro/`. Go into the patched folder, and we have some final work to do.
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```shellscript
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cd patch_libtorch_Allegro/
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```
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If you are using the Lin model, modify line 64 in `patch.py` to `tf_or_torch = ['cppflow']` and line 65 to `patch_model=['LCLIN']`. Then do the similar steps to those for the Allegro model. The patched code will be in `patch_cppflow_LCLIN` folder.
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# Step 6
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Finally, we need to modify the source code due to NERSC configuration:
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```shellscript
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```
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where `libnvrtc-builtins-7237cb5d.so.11.7` is a file in `/your_libtorch_path/libtorch/lib` and it is the source file or target of the link. This command is creating a symbolic link named `libnvrtc-builtins.so.11.7` that points to the source file `libnvrtc-builtins-7237cb5d.so.11.7`.
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<aside>
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⚠️ Note that this step may not be needed for NERSC, but will be necessary for gRASPA/Allegro to work on other universitys' clusters, depending on cluster's setup**
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⚠️ Note that this step may not be needed for NERSC, but will be necessary for gRASPA/Allegro to work on other universitys' clusters, depending on cluster's setup
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</aside>
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‎Examples/Ar_MgMOF74_Allegro/AllData/System_0/Component_0.data‎

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‎Examples/Ar_MgMOF74_Allegro/AllData/System_0/Component_1.data‎

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x y z charge scale scaleCoul Type

‎Examples/Ar_MgMOF74_Allegro/FirstBead/Energy.data‎

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PosA PosB TypeA TypeB E

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