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fix: Add ENV=TOLERATE_NUMERICAL_ERRORS=1 to GARD HyPhy command line #343

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Merged
stevenweaver merged 1 commit into from
Jan 12, 2026
Merged

fix: Add ENV=TOLERATE_NUMERICAL_ERRORS=1 to GARD HyPhy command line #343

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12 changes: 6 additions & 6 deletions app/gard/gard.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -80,20 +80,20 @@ if [ -n "$SLURM_JOB_ID" ]; then

if [ -f "$HYPHY_NON_MPI" ]; then
echo "Using non-MPI HYPHY: $HYPHY_NON_MPI"
echo "$HYPHY_NON_MPI LIBPATH=$HYPHY_PATH -z ENV=\"TOLERATE_NUMERICAL_ERRORS=1;\" $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE"
echo "$HYPHY_NON_MPI ENV=\"TOLERATE_NUMERICAL_ERRORS=1;\" LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE"
export TOLERATE_NUMERICAL_ERRORS=1
$HYPHY_NON_MPI LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
$HYPHY_NON_MPI ENV="TOLERATE_NUMERICAL_ERRORS=1;" LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
else
echo "Non-MPI HYPHY not found at $HYPHY_NON_MPI, attempting to use MPI version"
echo "srun --mpi=$MPI_TYPE -n $PROCS $HYPHY LIBPATH=$HYPHY_PATH -z ENV=\"TOLERATE_NUMERICAL_ERRORS=1;\" $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE"
echo "srun --mpi=$MPI_TYPE -n $PROCS $HYPHY ENV=\"TOLERATE_NUMERICAL_ERRORS=1;\" LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE"
export TOLERATE_NUMERICAL_ERRORS=1
srun --mpi=$MPI_TYPE -n $PROCS $HYPHY LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
srun --mpi=$MPI_TYPE -n $PROCS $HYPHY ENV="TOLERATE_NUMERICAL_ERRORS=1;" LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
fi
else
# Using mpirun for non-SLURM environments
echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH -z ENV=\"TOLERATE_NUMERICAL_ERRORS=1;\" $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE"
echo "mpirun -np $PROCS $HYPHY ENV=\"TOLERATE_NUMERICAL_ERRORS=1;\" LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE"
export TOLERATE_NUMERICAL_ERRORS=1
mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
mpirun -np $PROCS $HYPHY ENV="TOLERATE_NUMERICAL_ERRORS=1;" LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
fi

echo "Completed" > $STATUS_FILE
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