Changes to clarify usage

Text and variable name fo the OCI image targall durectory changed Sample directory paths changed to follow the CCR standard path naming policy Added a check for the podman binary - bail if missing Tidied some logic for the sample data directory Renamed the sample SLURM script to sample_SLURM_vasp_std.bash Tony
ubccr · Dec 5, 2024 · a0eb2ae · a0eb2ae
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diff --git a/slurm/2_ApplicationSpecific/VASP-GPU-podman/README.md b/slurm/2_ApplicationSpecific/VASP-GPU-podman/README.md
@@ -6,22 +6,22 @@ This is how to build VASP for GPU use, with a sample Slurm script
 
 To build VASP with nvidia GPU support takes about 45 minutes on a debug node.
 
-Get an interactive job on a debug node.
+Start an interactive job on a debug node.
 This example allcates a GPU to the job, but all tests are curenlty commented
 due to issues with using nvidia GPUs with "podman build"
 
 ```
 salloc --partition=debug --qos=debug --nodes=1 --gpus-per-node=1 --cpus-per-task=1 --tasks-per-node=32 --exclusive
 ```
 
-Create a directory for the podman image tarballs e.g.
+Create a directory for the podman OCI images e.g.
 ```
-mkdir -p /projects/academic/group/podman/images
+mkdir -p /projects/academic/ccrgroup/oci_archive_dir
 ```
 
 Create a directory for the podman scripts e.g.
 ```
-mkdir -p /projects/academic/group/VASP/bin
+mkdir -p /projects/academic/ccrgroup/VASP/bin
 ```
 
 Download the files to the Slurm temporary directory
@@ -33,7 +33,7 @@ wget https://github.com/tonykew/ccr-examples/raw/main/slurm/2_ApplicationSpecifi
 wget https://github.com/tonykew/ccr-examples/raw/main/slurm/2_ApplicationSpecific/VASP-GPU-podman/fix_nvhpc_.pc_files.bash
 wget https://github.com/tonykew/ccr-examples/raw/main/slurm/2_ApplicationSpecific/VASP-GPU-podman/run_vasp.bash
 wget https://github.com/tonykew/ccr-examples/raw/main/slurm/2_ApplicationSpecific/VASP-GPU-podman/run_vasp_shell.bash
-wget https://github.com/tonykew/ccr-examples/raw/main/slurm/2_ApplicationSpecific/VASP-GPU-podman/sample_vasp_std.bash
+wget https://github.com/tonykew/ccr-examples/raw/main/slurm/2_ApplicationSpecific/VASP-GPU-podman/sample_SLURM_vasp_std.bash
 chmod 755 build_vasp.bash fix_nvhpc_.pc_files.bash
 ```
 
@@ -51,34 +51,34 @@ Usage for the build script:
 
 ```
 ./build_vasp.bash 
-usage: ./build_vasp.bash image_tarball_directory bin_directory
+usage: ./build_vasp.bash oci_image_archive_directory bin_directory
 e.g.
-./build_vasp.bash /projects/academic/mygroup/podman_images/ /projects/academic/mygroup/VASP/bin
+./build_vasp.bash /projects/academic/ccrgroup/oci_archive_dir/ /projects/academic/ccrgroup/VASP/bin
 ```
 
 ...so, using the two directories created earlier:
 
 ```
-./build_vasp.bash /projects/academic/group/podman/images /projects/academic/group/VASP/bin
+./build_vasp.bash /projects/academic/ccrgroup/oci_archive_dir /projects/academic/ccrgroup/VASP/bin
 ```
 
 
 ## How to use
 
-There is a sample Slurm script in the scripts directory you
+There is a sample SLURM script in the scripts directory you
 provided for the build.
 e.g.
 
 ```
-/projects/academic/group/VASP/bin/sample_vasp_std.bash
+/projects/academic/ccrgroup/VASP/bin/sample_SLURM_vasp_std.bash
 ```
 
 copy the script, and change the "data_dir=" line to the directory with
 your data files in (i.e. "INCAR" etc.)
 e.g.
 
 ```
-data_dir="/projects/academic/group/username/data"
+data_dir="/projects/academic/ccrgroup/username/data"
 ```
 
 Make any other changes you might need to the #SBATCH options

diff --git a/slurm/2_ApplicationSpecific/VASP-GPU-podman/build_vasp.bash b/slurm/2_ApplicationSpecific/VASP-GPU-podman/build_vasp.bash
@@ -2,18 +2,18 @@
 
 if [ "${1}" = "" ] || [ ! -d "${1}" ] || [ "${2}" = "" ] || [ ! -d "${2}" ]
 then
-  echo "usage: ${0} image_tarball_directory bin_directory" >&2
+  echo "usage: ${0} oci_image_archive_directory bin_directory" >&2
   echo "e.g." >&2
-  echo "${0} /projects/academic/mygroup/podman_images/ /projects/academic/mygroup/VASP/bin" >&2
+  echo "${0} /projects/academic/ccrgroup/podman_images/ /projects/academic/ccrgroup/VASP/bin" >&2
   exit 1
 fi
 
-tarball_dir="${1}"
+oci_archive_dir="${1}"
 bin_dir="${2}"
 
-if [ "${tarball_dir}" = "" ] || [ ! -d "${tarball_dir}" ]
+if [ "${oci_archive_dir}" = "" ] || [ ! -d "${oci_archive_dir}" ]
 then
-  echo "image_tarball_directory \"${tarball_dir}\" doesn't exist - bailing" >&2
+  echo "image_oci_archive_directory \"${oci_archive_dir}\" doesn't exist - bailing" >&2
   exit 1
 fi
 
@@ -66,10 +66,10 @@ then
   exit 1
 fi
 
-echo "Saving container tarball"
+echo "Saving container OCI image"
 podman save \
  --format=oci-archive \
- --output="${tarball_dir}/podman-image-vasp-${vasp_version}-gpu-single-node.tar" \
+ --output="${oci_archive_dir}/podman-image-vasp-${vasp_version}-gpu-single-node.tar" \
  "localhost/vasp-${vasp_version}-gpu-single-node"
 
 echo "copying the run scripts"
@@ -78,7 +78,7 @@ then
   for prog_name in vasp_gam vasp_ncl vasp_std
   do
     sed -E -e "s|^vasp_version=.*|vasp_version=\"${vasp_version}\"|" \
-     -e "s|^image_tarball_dir=.*|image_tarball_dir=\"${tarball_dir}\"|" \
+     -e "s|^oci_archive_dir=.*|oci_archive_dir=\"${oci_archive_dir}\"|" \
      -e "s|VASP_PROG_NAME|${prog_name}|" \
      "run_vasp.bash" > "${bin_dir}/${prog_name}-${vasp_version}.bash"
     chmod 755 "${bin_dir}/${prog_name}-${vasp_version}.bash"
@@ -90,16 +90,22 @@ fi
 if [ -f "run_vasp_shell.bash" ]
 then
   sed -E -e "s|^vasp_version=.*|vasp_version=\"${vasp_version}\"|" \
-   -e "s|^image_tarball_dir=.*|image_tarball_dir=\"${tarball_dir}\"|" \
+   -e "s|^oci_archive_dir=.*|oci_archive_dir=\"${oci_archive_dir}\"|" \
    "run_vasp_shell.bash" > "${bin_dir}/run_vasp_shell-${vasp_version}.bash"
   chmod 755 "${bin_dir}/run_vasp_shell-${vasp_version}.bash"
   ln -sf "${bin_dir}/run_vasp_shell-${vasp_version}.bash" "${bin_dir}/run_vasp_shell"
 else
   echo "script \"run_vasp_shell.bash\" missing?" >&2
 fi
 # Provide a sample Slurm script
-if [ -f sample_vasp_std.bash ]
+if [ -f sample_SLURM_vasp_std.bash ]
 then
+  default_acct="$(sacctmgr -rnp show User "$(id -un)" | awk -F'|' '{print $2}')"
+  sed -E -i -e "/#SBATCH[[:space:]]+--account=/s|\".*\"|\"${default_acct}\"|" \
+   -e "/#SBATCH[[:space:]]+--chdir=/s|\".*\"|\"${base_dir}\"|" \
+   -e "s|^bin_dir=.*|bin_dir=\"${bin_dir}\"|" \
+   "sample_SLURM_vasp_std.bash"
+  # try to provide a reasonable data dir path
   grp_group="$(groups | sed 's/ /\n/g' | grep ^grp- | head -1 | sed 's/^grp-//')"
   if [ "${grp_group}" != "" ]
   then
@@ -112,16 +118,13 @@ then
         base_dir="/projects/rpci/${grp_group}/$(id -un)/VASP"
       fi
       default_acct="$(sacctmgr -rnp show User "$(id -un)" | awk -F'|' '{print $2}')"
-      sed -E -i -e "/#SBATCH[[:space:]]+--account=/s|\".*\"|\"${default_acct}\"|" \
-       -e "/#SBATCH[[:space:]]+--chdir=/s|\".*\"|\"${base_dir}\"|" \
-       -e "s|^bin_dir=.*|bin_dir=\"${bin_dir}\"|" \
-       -e "s|^data_dir=.*|data_dir=\"${base_dir}/data\"|" \
-       "sample_vasp_std.bash"
+      sed -E -i -e "s|^data_dir=.*|data_dir=\"${base_dir}/data\"|" \
+       "sample_SLURM_vasp_std.bash"
     fi
   fi
-  cp "sample_vasp_std.bash" "${bin_dir}/sample_vasp_std.bash"
+  cp "sample_SLURM_vasp_std.bash" "${bin_dir}/sample_SLURM_vasp_std.bash"
 else
-  echo "sample script \"sample_vasp_std.bash\" missing?" >&2
+  echo "sample script \"sample_SLURM_vasp_std.bash\" missing?" >&2
 fi
 echo
 
@@ -144,5 +147,5 @@ echo "  ${bin_dir}/run_vasp_shell"
 echo
 echo
 echo "Example Slurm script:"
-echo "  ${bin_dir}/sample_vasp_std.bash"
+echo "  ${bin_dir}/sample_SLURM_vasp_std.bash"
 echo
diff --git a/slurm/2_ApplicationSpecific/VASP-GPU-podman/run_vasp.bash b/slurm/2_ApplicationSpecific/VASP-GPU-podman/run_vasp.bash
@@ -2,14 +2,20 @@
 
 ##############################################################################
 vasp_version=""
-image_tarball_dir=""
+oci_archive_dir=""
 ##############################################################################
 
+if ! which podman > /dev/null 2>&1
+then
+  echo "podman not found - bailing" >&2
+  exit 1
+fi
+
 if ! podman image exists "localhost/vasp-${vasp_version}-gpu-single-node"
 then
   # load the image on this node
   echo "Loading the VASP image from the tarball - this takes some time..."
-  podman load --input "${image_tarball_dir}/podman-image-vasp-${vasp_version}-gpu-single-node.tar"
+  podman load --input "${oci_archive_dir}/podman-image-vasp-${vasp_version}-gpu-single-node.tar"
 fi
 
 # Run one MPI task per GPU (with one task per GPU)

diff --git a/slurm/2_ApplicationSpecific/VASP-GPU-podman/run_vasp_shell.bash b/slurm/2_ApplicationSpecific/VASP-GPU-podman/run_vasp_shell.bash
@@ -2,14 +2,20 @@
 
 ##############################################################################
 vasp_version=""
-image_tarball_dir=""
+oci_archive_dir=""
 ##############################################################################
 
+if ! which podman > /dev/null 2>&1
+then
+  echo "podman not found - bailing" >&2
+  exit 1
+fi
+
 if ! podman image exists "localhost/vasp-${vasp_version}-gpu-single-node"
 then
   # load the image on this node
   echo "Loading the VASP image from the tarball - this takes some time..."
-  podman load --input "${image_tarball_dir}/podman-image-vasp-${vasp_version}-gpu-single-node.tar"
+  podman load --input "${oci_archive_dir}/podman-image-vasp-${vasp_version}-gpu-single-node.tar"
 fi
 
 # Run one MPI task per GPU (with one task per GPU)

diff --git a/...ific/VASP-GPU-podman/sample_vasp_std.bash → ...ASP-GPU-podman/sample_SLURM_vasp_std.bash b/...ific/VASP-GPU-podman/sample_vasp_std.bash → ...ASP-GPU-podman/sample_SLURM_vasp_std.bash
@@ -1,7 +1,7 @@
 #!/bin/bash -l
 
 # Slurm account
-#SBATCH --account="ccradmin"
+#SBATCH --account="ccrgroup"
 
 #SBATCH --clusters=ub-hpc
 #SBATCH --partition=general-compute --qos=general-compute
@@ -10,16 +10,14 @@
 #SBATCH --gpus-per-node=1
 #SBATCH --exclusive
 #SBATCH --output=%j.out
-# 30 minutes  walltime
+# 1 hour walltime
 #SBATCH --time=01:00:00
 
-# directory in which to write job output file [job_id].out:
-#SBATCH --chdir="/projects/academic/tonykew/tonykew/VASP"
+# Path to the vasp support scipts (you shouldn't need change this)
+bin_dir="/projects/academic/ccrgroup/VASP/bin"
 
-##############################################################################
-bin_dir="/vscratch/grp-tonykew/VASP/bin"
-data_dir="/projects/academic/tonykew/tonykew/VASP/data"
-##############################################################################
+# Configure the VASP data directory here:
+data_dir="/projects/academic/ccrgroup/ccruser/VASP/data"
 
 echo "-------------------------------------------------------------------------------"
 echo "Job info:"
@@ -72,11 +70,6 @@ if [ "${SLURM_NTASKS_PER_GPU}" != "" ]
 then
   echo "Tasks per GPU: ${SLURM_NTASKS_PER_GPU}"
 fi
-## Infiniband is not used, so the Slurm topology is irrelevant
-#if [ "{SLURM_TOPOLOGY_ADDR}"  != "" ]
-#then
-#  echo "SLURM topology: ${SLURM_TOPOLOGY_ADDR}"
-#fi
 echo
 echo "-------------------------------------------------------------------------------"
 echo