This is an automated email from the ASF dual-hosted git repository. yasith pushed a commit to branch sdk-batch-jobs in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 77d93be30b2311c1800e44a5449aec18965fcb96 Author: yasithdev <[email protected]> AuthorDate: Sun Aug 3 00:16:18 2025 -0500 bump version to 2.2.2, fix bug in namd.sh --- .../airavata_experiments/airavata.py | 4 ++-- dev-tools/airavata-python-sdk/pyproject.toml | 2 +- .../airavata-agent/application/namd.sh | 28 ++++++++++------------ 3 files changed, 16 insertions(+), 18 deletions(-) diff --git a/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py b/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py index fd83596c08..8dbebd6b5e 100644 --- a/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py +++ b/dev-tools/airavata-python-sdk/airavata_experiments/airavata.py @@ -412,7 +412,7 @@ class AiravataOperator: """ import os - fp = os.path.join("/data", remote_file) + fp = os.path.join(".", remote_file) res = requests.post(f"{self.connection_svc_url()}/agent/execute/shell", json={ "agentId": agent_ref, "envName": agent_ref, @@ -487,7 +487,7 @@ class AiravataOperator: """ import os - fp = os.path.join("/data", remote_file) + fp = os.path.join(".", remote_file) res = requests.post(f"{self.connection_svc_url()}/agent/execute/shell", json={ "agentId": agent_ref, "envName": agent_ref, diff --git a/dev-tools/airavata-python-sdk/pyproject.toml b/dev-tools/airavata-python-sdk/pyproject.toml index 148b2597f9..04620578c0 100644 --- a/dev-tools/airavata-python-sdk/pyproject.toml +++ b/dev-tools/airavata-python-sdk/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "airavata-python-sdk" -version = "2.2.1" +version = "2.2.2" description = "Apache Airavata Python SDK" readme = "README.md" license = "Apache-2.0" diff --git a/modules/agent-framework/airavata-agent/application/namd.sh b/modules/agent-framework/airavata-agent/application/namd.sh index fd1297b23b..240cc2ad10 100644 --- a/modules/agent-framework/airavata-agent/application/namd.sh +++ b/modules/agent-framework/airavata-agent/application/namd.sh @@ -10,6 +10,14 @@ export CS_HOME=$HOME/cybershuttle export MAMBA_ROOT_PREFIX=$CS_HOME/scratch export TMPDIR=$CS_HOME/scratch/tmp +# initialize scratch/tmp and scratch/envs (node-local) +CS_TEMP=$(readlink $CS_HOME/scratch/tmp) +CS_ENVS=$(readlink $CS_HOME/scratch/envs) +[ -n "$CS_TEMP" ] && mkdir -p $CS_TEMP +[ -n "$CS_ENVS" ] && mkdir -p $CS_ENVS +NAMD_EXTRA_ARGS=() +FIFO=$(mktemp -u) +mkfifo $FIFO # ---------------------------------------------------------------------- # PARSE COMMAND LINE ARGUMENTS @@ -35,12 +43,12 @@ while getopts t:n:i:a:s: option; do module reset if [ $EXECUTION_TYPE = "CPU" ]; then # one replica at a time - echo 0 > $FIFO + echo 0 > $FIFO & NAMD_PATH=$NAMD_CPU_PATH module load $NAMD_CPU_MODULES elif [ $EXECUTION_TYPE = "GPU" ]; then # one replica per GPU - for ((i=0; i<SLURM_GPUS_ON_NODE; i++)); do echo "$i" > $FIFO; done + for ((i=0; i<${SLURM_GPUS_ON_NODE:-0}; i++)); do echo "$i" > $FIFO & done NAMD_PATH=$NAMD_GPU_PATH NAMD_EXTRA_ARGS+=("--CUDASOAintegrate" "on") module load $NAMD_GPU_MODULES @@ -52,7 +60,7 @@ while getopts t:n:i:a:s: option; do echo "NUM_REPLICAS=$NUM_REPLICAS" ;; i) - NAMD_INPUT_FILES=$(find $WORKDIR -maxdepth 1 -type f ! -name "*slurm*") + NAMD_INPUT_FILES=$(find $WORKDIR -maxdepth 1 -type f ! -name "*slurm*" ! -name "*.stdout" ! -name "*.stderr") NAMD_CONF_FILE=$OPTARG echo "NAMD_INPUT_FILES=$NAMD_INPUT_FILES" echo "NAMD_CONF_FILE=$NAMD_CONF_FILE" @@ -82,21 +90,11 @@ shift $((OPTIND - 1)) # RUN AGENT # ---------------------------------------------------------------------- -# initialize scratch/tmp and scratch/envs (node-local) -CS_TEMP=$(readlink $CS_HOME/scratch/tmp) -CS_ENVS=$(readlink $CS_HOME/scratch/envs) -[ -n "$CS_TEMP" ] && mkdir -p $CS_TEMP -[ -n "$CS_ENVS" ] && mkdir -p $CS_ENVS - -NAMD_EXTRA_ARGS=() -FIFO=$(mktemp -u) -mkfifo $FIFO - wget -q https://github.com/cyber-shuttle/binaries/releases/download/1.0.1/airavata-agent-linux-amd64 -O $WORKDIR/airavata-agent wget -q https://github.com/cyber-shuttle/binaries/releases/download/1.0.1/kernel.py -O $WORKDIR/kernel.py wget -q https://github.com/mamba-org/micromamba-releases/releases/download/2.3.0-1/micromamba-linux-64 -O $WORKDIR/micromamba chmod +x $WORKDIR/airavata-agent $WORKDIR/micromamba -$WORKDIR/airavata-agent --server "$AGENT_SERVER:19900" --agent "$AGENT_ID" --environ base --lib "" --pip "" & +$WORKDIR/airavata-agent --server "$AGENT_SERVER:19900" --agent "$AGENT_ID" --environ "$AGENT_ID" --lib "" --pip "" & AGENT_PID=$! trap 'kill -TERM $AGENT_PID' EXIT echo "Agent started with PID $AGENT_PID" @@ -119,7 +117,7 @@ for REPLICA_ID in $(seq 1 $NUM_REPLICAS); do $REPLICA_DIR/$NAMD_CONF_FILE >$REPLICA_DIR/$NAMD_CONF_FILE.out 2>$REPLICA_DIR/$NAMD_CONF_FILE.err [[ $EXECUTION_TYPE == "GPU" ]] && unset CUDA_VISIBLE_DEVICES - echo $TOKEN > $FIFO + echo $TOKEN > $FIFO & for FILE in $(ls $REPLICA_DIR/*.*); do mv $FILE $REPLICA_ID"_"$(basename $FILE)
