Installation CP2K

[Esam Elkandro]

Dear cp2k community,

I installed the cp2k under our three clusters and every time I don't get executable file "cp2k.psmp" to use it.  Even though, I run my calculations by using "cp2k.popt", however, these calculations is very slow and I don't see any difference if I use multi node comparing single node.  How to install the executable file "psmp"?  

Hint:  Our cluster has  more than 50 nodes and each node has 64 CPU.

Please check my installation steps in two different clusters:

#### 1st way ########

conda create --name cp2k
conda activate cp2k
conda install -c conda-forge cp2k
conda install -c conda-forge/label/cf202003 cp2k
conda update -n base -c defaults conda

#### 2nd way ########

source /opt/intel/bin/ifortvars.sh intel64
 
wget https://github.com/cp2k/cp2k/releases/download/v5.1.0/cp2k-5.1.tar.bz2
tar xvf cp2k-5.1.tar.bz2
cd cp2k-5.1/tools/toolchain/
./install_cp2k_toolchain.sh --install-all --with-mkl=system

cd ~
cp /root/cp2k-5.1/tools/toolchain/install/arch/* cp2k-5.1/arch/
source /root/cp2k-5.1/tools/toolchain/install/setup
 
cd cp2k-5.1
make -j 28 ARCH=local VERSION="sopt sdbg ssmp popt pdbg "

Best,

Esam

[Jeff Terstriep]

You only want to use the 'conda install -c conda-forge cp2k' command. The second conda install using the label installs the much older cp2k 6.1.

That said, cp2k installs the single-node version. If you want cp2k.psmp using MPI, install with 'conda install -c conda-forge cp2k=8.2.0=py38_openmpi_1'. Search anaconda.org for cp2k and look under the files tab to see the latest version and build data.

Jeff

[Esam Elkandro]

Hi Travis and thanks for your help.

I have already installed "psmp" and it only works under single node. I tried increasing the number of processors, but it does not work and I thought something was wrong during the installation.

On Tuesday, June 15, 2021 at 12:22:28 PM UTC-5 Travis wrote:

Hi,

Not sure about your first method, the most recent conda-forge cp2k packages only have psmp in bin/. But in the second method, you don't request to install the psmp version just popt and pdbg.

-T

[Esam Elkandro]

Thank you so much Jeff.

I follow your suggestion about " conda install -c conda-forge cp2k=8.2.0=py38_openmpi_1" and the installation  was successful with "cp2k.psmp".

After installation, I got this message " mpiexec --mca opal_cuda_support 1" what does this mean?

Here is my job file:

#!/bin/bash
#SBATCH -J MPI
#SBATCH --nodes=2
#SBATCH --ntasks=64
#SBATCH --time=0-24:00:00
#SBATCH --export=all
#SBATCH --out=Foundry-%j.out


module load openmpi/4.0.3/intel/2020.0
module load anaconda/2020.7
source activate cp2k
####mpiexec --mca opal_cuda_support -np 128 cp2k.psmp -i NVE_md.inp -o md4.out

mpiexec -np 128 cp2k.psmp -i NVE_md.inp -o md4.out

##### After installation ####

"Preparing transaction: done
Verifying transaction: done
Executing transaction: |
For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default.
To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
Equivalently, you can set the MCA parameters in the command line:
mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
Please consult UCX's documentation for detail."

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[Esam Elkandro]

I have an issue with the "libint" library and please see the attached file.

Best,

Esam