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stevenweaverstevenweaver
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fix: Force all analysis methods to use HYPHYMP (non-MPI) exclusively
- Remove MPI dependency from all datamonkey analysis scripts - Always use HYPHYMP instead of HYPHYMPI to avoid libmpi.so.40 errors - Compute nodes don't have lmod, so MPI modules can't be loaded anyway - Applied to: absrel, bgm, busted, cfel, fade, fel, fubar, gard, meme, multihit, nrm, relax, slac
1 parent edccb03 commit 926c7df

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13 files changed

+78
-156
lines changed

13 files changed

+78
-156
lines changed

‎app/absrel/absrel.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -97,20 +97,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
9797
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
9898

9999
# Check which HYPHY version to use
100-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
101-
# Local execution and regular hyphy exists - use it
102-
HYPHY=$HYPHY_REGULAR
103-
echo "Using regular HYPHY for local execution: $HYPHY"
104-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
105-
# Local execution and non-MPI version exists - use it
100+
# Always use non-MPI version for datamonkey jobs
101+
if [ -f "$HYPHY_NON_MPI" ]; then
106102
HYPHY=$HYPHY_NON_MPI
107-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
108-
elif [ -f "$HYPHY_MPI" ]; then
109-
# Use MPI version (for cluster execution or if others not available)
110-
HYPHY=$HYPHY_MPI
111-
echo "Using MPI HYPHY: $HYPHY"
103+
echo "Using non-MPI HYPHY: $HYPHY"
104+
elif [ -f "$HYPHY_REGULAR" ]; then
105+
HYPHY=$HYPHY_REGULAR
106+
echo "Using regular HYPHY: $HYPHY"
112107
else
113-
# Fallback - try to find any HYPHY executable
114108
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
115109
echo "Using fallback HYPHY: $HYPHY"
116110
fi

‎app/bgm/bgm.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -119,20 +119,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
119119
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
120120

121121
# Check which HYPHY version to use
122-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
123-
# Local execution and regular hyphy exists - use it
124-
HYPHY=$HYPHY_REGULAR
125-
echo "Using regular HYPHY for local execution: $HYPHY"
126-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
127-
# Local execution and non-MPI version exists - use it
122+
# Always use non-MPI version for datamonkey jobs
123+
if [ -f "$HYPHY_NON_MPI" ]; then
128124
HYPHY=$HYPHY_NON_MPI
129-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
130-
elif [ -f "$HYPHY_MPI" ]; then
131-
# Use MPI version (for cluster execution or if others not available)
132-
HYPHY=$HYPHY_MPI
133-
echo "Using MPI HYPHY: $HYPHY"
125+
echo "Using non-MPI HYPHY: $HYPHY"
126+
elif [ -f "$HYPHY_REGULAR" ]; then
127+
HYPHY=$HYPHY_REGULAR
128+
echo "Using regular HYPHY: $HYPHY"
134129
else
135-
# Fallback - try to find any HYPHY executable
136130
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
137131
echo "Using fallback HYPHY: $HYPHY"
138132
fi

‎app/busted/busted_submit.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -120,20 +120,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
120120
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
121121

122122
# Check which HYPHY version to use
123-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
124-
# Local execution and regular hyphy exists - use it
125-
HYPHY=$HYPHY_REGULAR
126-
echo "Using regular HYPHY for local execution: $HYPHY"
127-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
128-
# Local execution and non-MPI version exists - use it
123+
# Always use non-MPI version for datamonkey jobs
124+
if [ -f "$HYPHY_NON_MPI" ]; then
129125
HYPHY=$HYPHY_NON_MPI
130-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
131-
elif [ -f "$HYPHY_MPI" ]; then
132-
# Use MPI version (for cluster execution or if others not available)
133-
HYPHY=$HYPHY_MPI
134-
echo "Using MPI HYPHY: $HYPHY"
126+
echo "Using non-MPI HYPHY: $HYPHY"
127+
elif [ -f "$HYPHY_REGULAR" ]; then
128+
HYPHY=$HYPHY_REGULAR
129+
echo "Using regular HYPHY: $HYPHY"
135130
else
136-
# Fallback - try to find any HYPHY executable
137131
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
138132
echo "Using fallback HYPHY: $HYPHY"
139133
fi

‎app/contrast-fel/cfel.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -104,20 +104,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
104104
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
105105

106106
# Check which HYPHY version to use
107-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
108-
# Local execution and regular hyphy exists - use it
109-
HYPHY=$HYPHY_REGULAR
110-
echo "Using regular HYPHY for local execution: $HYPHY"
111-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
112-
# Local execution and non-MPI version exists - use it
107+
# Always use non-MPI version for datamonkey jobs
108+
if [ -f "$HYPHY_NON_MPI" ]; then
113109
HYPHY=$HYPHY_NON_MPI
114-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
115-
elif [ -f "$HYPHY_MPI" ]; then
116-
# Use MPI version (for cluster execution or if others not available)
117-
HYPHY=$HYPHY_MPI
118-
echo "Using MPI HYPHY: $HYPHY"
110+
echo "Using non-MPI HYPHY: $HYPHY"
111+
elif [ -f "$HYPHY_REGULAR" ]; then
112+
HYPHY=$HYPHY_REGULAR
113+
echo "Using regular HYPHY: $HYPHY"
119114
else
120-
# Fallback - try to find any HYPHY executable
121115
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
122116
echo "Using fallback HYPHY: $HYPHY"
123117
fi

‎app/fade/fade.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -117,20 +117,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
117117
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
118118

119119
# Check which HYPHY version to use
120-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
121-
# Local execution and regular hyphy exists - use it
122-
HYPHY=$HYPHY_REGULAR
123-
echo "Using regular HYPHY for local execution: $HYPHY"
124-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
125-
# Local execution and non-MPI version exists - use it
120+
# Always use non-MPI version for datamonkey jobs
121+
if [ -f "$HYPHY_NON_MPI" ]; then
126122
HYPHY=$HYPHY_NON_MPI
127-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
128-
elif [ -f "$HYPHY_MPI" ]; then
129-
# Use MPI version (for cluster execution or if others not available)
130-
HYPHY=$HYPHY_MPI
131-
echo "Using MPI HYPHY: $HYPHY"
123+
echo "Using non-MPI HYPHY: $HYPHY"
124+
elif [ -f "$HYPHY_REGULAR" ]; then
125+
HYPHY=$HYPHY_REGULAR
126+
echo "Using regular HYPHY: $HYPHY"
132127
else
133-
# Fallback - try to find any HYPHY executable
134128
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
135129
echo "Using fallback HYPHY: $HYPHY"
136130
fi

‎app/fel/fel.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -109,20 +109,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
109109
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
110110

111111
# Check which HYPHY version to use
112-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
113-
# Local execution and regular hyphy exists - use it
114-
HYPHY=$HYPHY_REGULAR
115-
echo "Using regular HYPHY for local execution: $HYPHY"
116-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
117-
# Local execution and non-MPI version exists - use it
112+
# Always use non-MPI version for datamonkey jobs
113+
if [ -f "$HYPHY_NON_MPI" ]; then
118114
HYPHY=$HYPHY_NON_MPI
119-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
120-
elif [ -f "$HYPHY_MPI" ]; then
121-
# Use MPI version (for cluster execution or if others not available)
122-
HYPHY=$HYPHY_MPI
123-
echo "Using MPI HYPHY: $HYPHY"
115+
echo "Using non-MPI HYPHY: $HYPHY"
116+
elif [ -f "$HYPHY_REGULAR" ]; then
117+
HYPHY=$HYPHY_REGULAR
118+
echo "Using regular HYPHY: $HYPHY"
124119
else
125-
# Fallback - try to find any HYPHY executable
126120
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
127121
echo "Using fallback HYPHY: $HYPHY"
128122
fi

‎app/fubar/fubar.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -77,20 +77,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
7777
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
7878

7979
# Check which HYPHY version to use
80-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
81-
# Local execution and regular hyphy exists - use it
82-
HYPHY=$HYPHY_REGULAR
83-
echo "Using regular HYPHY for local execution: $HYPHY"
84-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
85-
# Local execution and non-MPI version exists - use it
80+
# Always use non-MPI version for datamonkey jobs
81+
if [ -f "$HYPHY_NON_MPI" ]; then
8682
HYPHY=$HYPHY_NON_MPI
87-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
88-
elif [ -f "$HYPHY_MPI" ]; then
89-
# Use MPI version (for cluster execution or if others not available)
90-
HYPHY=$HYPHY_MPI
91-
echo "Using MPI HYPHY: $HYPHY"
83+
echo "Using non-MPI HYPHY: $HYPHY"
84+
elif [ -f "$HYPHY_REGULAR" ]; then
85+
HYPHY=$HYPHY_REGULAR
86+
echo "Using regular HYPHY: $HYPHY"
9287
else
93-
# Fallback - try to find any HYPHY executable
9488
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
9589
echo "Using fallback HYPHY: $HYPHY"
9690
fi

‎app/gard/gard.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -105,20 +105,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
105105
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
106106

107107
# Check which HYPHY version to use
108-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
109-
# Local execution and regular hyphy exists - use it
110-
HYPHY=$HYPHY_REGULAR
111-
echo "Using regular HYPHY for local execution: $HYPHY"
112-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
113-
# Local execution and non-MPI version exists - use it
108+
# Always use non-MPI version for datamonkey jobs
109+
if [ -f "$HYPHY_NON_MPI" ]; then
114110
HYPHY=$HYPHY_NON_MPI
115-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
116-
elif [ -f "$HYPHY_MPI" ]; then
117-
# Use MPI version (for cluster execution or if others not available)
118-
HYPHY=$HYPHY_MPI
119-
echo "Using MPI HYPHY: $HYPHY"
111+
echo "Using non-MPI HYPHY: $HYPHY"
112+
elif [ -f "$HYPHY_REGULAR" ]; then
113+
HYPHY=$HYPHY_REGULAR
114+
echo "Using regular HYPHY: $HYPHY"
120115
else
121-
# Fallback - try to find any HYPHY executable
122116
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
123117
echo "Using fallback HYPHY: $HYPHY"
124118
fi

‎app/meme/meme.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -109,20 +109,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
109109
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
110110

111111
# Check which HYPHY version to use
112-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
113-
# Local execution and regular hyphy exists - use it
114-
HYPHY=$HYPHY_REGULAR
115-
echo "Using regular HYPHY for local execution: $HYPHY"
116-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
117-
# Local execution and non-MPI version exists - use it
112+
# Always use non-MPI version for datamonkey jobs
113+
if [ -f "$HYPHY_NON_MPI" ]; then
118114
HYPHY=$HYPHY_NON_MPI
119-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
120-
elif [ -f "$HYPHY_MPI" ]; then
121-
# Use MPI version (for cluster execution or if others not available)
122-
HYPHY=$HYPHY_MPI
123-
echo "Using MPI HYPHY: $HYPHY"
115+
echo "Using non-MPI HYPHY: $HYPHY"
116+
elif [ -f "$HYPHY_REGULAR" ]; then
117+
HYPHY=$HYPHY_REGULAR
118+
echo "Using regular HYPHY: $HYPHY"
124119
else
125-
# Fallback - try to find any HYPHY executable
126120
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
127121
echo "Using fallback HYPHY: $HYPHY"
128122
fi

‎app/multihit/multihit.sh‎

Lines changed: 6 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -93,20 +93,14 @@ HYPHY_NON_MPI=$CWD/../../.hyphy/HYPHYMP
9393
HYPHY_MPI=$CWD/../../.hyphy/HYPHYMPI
9494

9595
# Check which HYPHY version to use
96-
if [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_REGULAR" ]; then
97-
# Local execution and regular hyphy exists - use it
98-
HYPHY=$HYPHY_REGULAR
99-
echo "Using regular HYPHY for local execution: $HYPHY"
100-
elif [ -z "$SLURM_JOB_ID" ] && [ -f "$HYPHY_NON_MPI" ]; then
101-
# Local execution and non-MPI version exists - use it
96+
# Always use non-MPI version for datamonkey jobs
97+
if [ -f "$HYPHY_NON_MPI" ]; then
10298
HYPHY=$HYPHY_NON_MPI
103-
echo "Using non-MPI HYPHY for local execution: $HYPHY"
104-
elif [ -f "$HYPHY_MPI" ]; then
105-
# Use MPI version (for cluster execution or if others not available)
106-
HYPHY=$HYPHY_MPI
107-
echo "Using MPI HYPHY: $HYPHY"
99+
echo "Using non-MPI HYPHY: $HYPHY"
100+
elif [ -f "$HYPHY_REGULAR" ]; then
101+
HYPHY=$HYPHY_REGULAR
102+
echo "Using regular HYPHY: $HYPHY"
108103
else
109-
# Fallback - try to find any HYPHY executable
110104
HYPHY=$(which hyphy 2>/dev/null || echo "$CWD/../../.hyphy/hyphy")
111105
echo "Using fallback HYPHY: $HYPHY"
112106
fi

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