Fix Slurm Scripts that Submit MDTools Scripts

analysis/lintf2_ether/gmx/.cleanup_gmx_analyses.sh

@@ -2,37 +2,35 @@
 
 # Cleanup the analysis directory after all analyses have finished.
 #
-# * Remove *_slurm-* suffix in directory names.
+# * Remove *_slurm-[0-9]* suffix in directory names.
 # * Move similar analyses into one directory.
 
 gather() {
     # Gather output of similar analyses scripts.
-    root="${1}"
-    mkdir "${root}" || exit
-    mv "${root}"_* "${root}"/
-    cd "${root}"/ || exit
-    mv "${root}"_*/* ./
-    rm -r "${root}"_*
-    cd ../ || exit
+    local root="${1}"
+    if [[ -d ${root} ]]; then
+        echo "WARNING: Directory already exists: '${root}'"
+        return 0
+    fi
+    if [[ -n $(find . -maxdepth 1 -type d -name "${root}*_slurm-[0-9]*" -print -quit) ]]; then
+        mkdir "${root}/" || exit
+        mv "${root}"*_slurm-[0-9]*/ "${root}/" || exit
+        cd "${root}/" || exit
+        mv "${root}"*_slurm-[0-9]*/* ./ || exit
+        rm -r "${root:?}"*_slurm-[0-9]*/ || exit
+        cd ../ || exit
+    else
+        echo "WARNING: No directory matching pattern '${root}*_slurm-[0-9]*'"
+    fi
 }
 
-mv energy_slurm-* energy
-mv make_ndx_slurm-* make_ndx
-mv polystat_slurm-* polystat
-mv potential-z_slurm-* potential-z
-
-gather density-z
-gather densmap-z
-gather msd
-gather trjconv
-
-name1=rdf
-name2=rdf_slab-z
-gather "${name2}"
-mkdir "${name1}" || exit
-mv "${name1}"_* "${name1}"/
-cd "${name1}"/ || exit
-mv "${name2}"/ ../
-mv "${name1}"_*/* ./
-rm -r "${name1}"_*
-cd ../ || exit
+gather "density-z"
+gather "densmap-z"
+gather "energy"
+gather "make_ndx"
+gather "msd"
+gather "polystat"
+gather "potential-z"
+gather "rdf_slab-z"
+gather "rdf"
+gather "trjconv"

analysis/lintf2_ether/mdt/.cleanup_mdt_analyses.sh

@@ -2,120 +2,84 @@
 
 # Cleanup the analysis directory after all analyses have finished.
 #
-# * Remove *_slurm-* suffix in directory names.
+# * Remove *_slurm-[0-9]* suffix in directory names.
 # * Move similar analyses into one directory.
 
 gather() {
     # Gather output of similar analyses scripts.
-    root="${1}"
-    mkdir "${root}" || exit
-    mv "${root}"_* "${root}"/
-    cd "${root}"/ || exit
-    mv "${root}"_*/* ./
-    rm -r "${root}"_*
-    cd ../ || exit
+    local root="${1}"
+    if [[ -d ${root} ]]; then
+        echo "WARNING: Directory already exists: '${root}'"
+        return 0
+    fi
+    if [[ -n $(find . -maxdepth 1 -type d -name "${root}*_slurm-[0-9]*" -print -quit) ]]; then
+        mkdir "${root}/" || exit
+        mv "${root}"*_slurm-[0-9]*/ "${root}/" || exit
+        cd "${root}/" || exit
+        mv "${root}"*_slurm-[0-9]*/* ./ || exit
+        rm -r "${root:?}"*_slurm-[0-9]*/ || exit
+        cd ../ || exit
+    else
+        echo "WARNING: No directory matching pattern '${root}*_slurm-[0-9]*'"
+    fi
 }
 
-mv create_mda_universe_slurm-* create_mda_universe
-mv energy_dist_slurm-* energy_dist
-mv subvolume_charge_slurm-* subvolume_charge
+gather_cmps() {
+    # Gather output of similar analyses scripts ordered by compounds
+    # into sub-directories.
+    local root="${1}"
+    local cmps="${2}"
 
-gather discrete-z
-gather lifetime_autocorr
+    # Create "root" directory.
+    if [[ -d ${root} ]]; then
+        echo "WARNING: Directory already exists: '${root}'"
+        return 0
+    else
+        mkdir "${root}/" || exit
+    fi
 
-name=attribute_hist
-for cmp in Li NBT OBT OE NTf2 ether; do
-    gather "${name}"_"${cmp}"
-done
-mkdir "${name}" || exit
-mv "${name}"_* "${name}"/
+    # Move all "compound" directories to the root directory.
+    for cmp in ${cmps}; do
+        if [[ -n $(find . -maxdepth 1 -type d -name "${root}_${cmp}*_slurm-[0-9]*" -print -quit) ]]; then
+            mv "${root}_${cmp}"*_slurm-[0-9]*/ "${root}/" || exit
+        fi
+    done
 
-name=axial_hex_dist
-for cmp in 1nn 2nn; do
-    gather "${name}"_"${cmp}"
-done
-mkdir "${name}" || exit
-mv "${name}"_* "${name}"/
+    # Check if the root directory is empty.
+    if [[ -n $(find "${root}/" -prune -empty) ]]; then
+        echo "WARNING: No directory matching pattern '${root}_<compound>*_slurm-[0-9]*'"
+        rm -r "${root:?}/" || exit
+        return 0
+    fi
 
-name=discrete_hex
-for cmp in Li NBT OBT OE; do
-    gather "${name}"_"${cmp}"
-done
-mkdir "${name}" || exit
-mv "${name}"_* "${name}"/
+    # Gather all compound analyses.
+    cd "${root}/" || exit
+    for cmp in ${cmps}; do
+        gather "${root}_${cmp}"
+    done
+    cd ../ || exit
+}
 
-name=renewal_events
-for cmp in Li-ether Li-NTf2; do
-    gather "${name}"_"${cmp}"
-done
-mkdir "${name}" || exit
-mv "${name}"_* "${name}"/
+gather "create_mda_universe"
+gather "energy_dist"
+gather "lifetime_autocorr"
+gather "lig_change_at_pos_change_blocks_hist"
+gather "lig_change_at_pos_change_blocks"
+gather "lig_change_at_pos_change"
+gather "subvolume_charge"
 
-name=topo_map
-for cmp in Li-OBT Li-OE; do
-    gather "${name}"_"${cmp}"
-done
-mkdir "${name}" || exit
-mv "${name}"_* "${name}"/
+gather_cmps "attribute_hist" "Li NBT OBT OE NTf2 ether"
+gather_cmps "axial_hex_dist" "1nn 2nn"
+gather_cmps "renewal_events" "Li-ether Li-NTf2"
+gather_cmps "topo_map" "Li-OBT Li-OE"
 
-name1=contact_hist
-name2=contact_hist_at_pos_change
-name3=contact_hist_slab-z
-gather "${name2}"
-for cmp in Li-OBT Li-OE; do
-    gather "${name3}"_"${cmp}"
-done
-mkdir "${name3}" || exit
-mv "${name3}"_* "${name3}"/
-mkdir "${name1}" || exit
-mv "${name1}"_* "${name1}"/
-cd "${name1}"/ || exit
-mv "${name2}"/ "${name3}"/ ../
-mv "${name1}"_*/* ./
-rm -r "${name1}"_*
-cd ../ || exit
+gather_cmps "contact_hist_slab-z" "Li-OBT Li-OE"
+gather "contact_hist_at_pos_change"
+gather "contact_hist"
 
-name1=msd
-name2=msd_at_coord_change
-name3=msd_layer
-gather "${name2}"
-gather "${name3}"
-cd "${name3}" || exit
-for cmp in ether Li NBT NTf2 OBT OE; do
-    for file in *_"${cmp}"_slurm-*; do
-        if [[ -f ${file} ]]; then
-            mkdir "${name3}"_"${cmp}" || exit
-            mv ./*_"${cmp}"_* "${name3}"_"${cmp}"/
-            break
-        fi
-    done
-done
-cd ../ || exit
-mkdir "${name1}" || exit
-mv "${name1}"_* "${name1}"/
-cd "${name1}"/ || exit
-mv "${name2}"/ "${name3}"/ ../
-mv "${name1}"_*/* ./
-rm -r "${name1}"_*
-cd ../ || exit
+gather_cmps "discrete_hex" "Li NBT OBT OE"
+gather "discrete-z"
 
-name1=lig_change_at_pos_change_blocks
-name2=lig_change_at_pos_change_blocks_hist
-gather "${name2}"
-mkdir "${name1}" || exit
-mv "${name1}"_* "${name1}"/
-cd "${name1}"/ || exit
-mv "${name2}"/ ../
-mv "${name1}"_*/* ./
-rm -r "${name1}"_*
-cd ../ || exit
-name1=lig_change_at_pos_change
-name2=lig_change_at_pos_change_blocks
-name3=lig_change_at_pos_change_blocks_hist
-mkdir "${name1}" || exit
-mv "${name1}"_* "${name1}"/
-cd "${name1}"/ || exit
-mv "${name2}"/ "${name3}"/ ../
-mv "${name1}"_*/* ./
-rm -r "${name1}"_*
-cd ../ || exit
+gather_cmps "msd_layer" "Li NBT OBT OE NTf2 ether"
+gather "msd_at_coord_change"
+gather "msd"

analysis/lintf2_ether/mdt/attribute_hist_Li.sh

@@ -5,7 +5,7 @@
 #SBATCH --output="mdt_attribute_hist_Li_slurm-%j.out"
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=4G
+#SBATCH --mem=1G
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/attribute_hist_NBT.sh

@@ -5,7 +5,7 @@
 #SBATCH --output="mdt_attribute_hist_NBT_slurm-%j.out"
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=4G
+#SBATCH --mem=1G
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/attribute_hist_NTf2.sh

@@ -5,7 +5,7 @@
 #SBATCH --output="mdt_attribute_hist_NTf2_slurm-%j.out"
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=12G
+#SBATCH --mem=2G
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/attribute_hist_OBT.sh

@@ -5,7 +5,7 @@
 #SBATCH --output="mdt_attribute_hist_OBT_slurm-%j.out"
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=8G
+#SBATCH --mem=2G
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/attribute_hist_OE.sh

@@ -5,7 +5,7 @@
 #SBATCH --output="mdt_attribute_hist_OE_slurm-%j.out"
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=12G
+#SBATCH --mem=2G
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/attribute_hist_ether.sh

@@ -5,7 +5,7 @@
 #SBATCH --output="mdt_attribute_hist_ether_slurm-%j.out"
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=16G
+#SBATCH --mem=2G
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/contact_hist_Li-O.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=2-00:00:00
+#SBATCH --time=7-00:00:00
 #SBATCH --job-name="mdt_contact_hist_Li-O"
 #SBATCH --output="mdt_contact_hist_Li-O_slurm-%j.out"
 #SBATCH --nodes=1
-#SBATCH --cpus-per-task=2
-#SBATCH --mem=1G
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/contact_hist_Li-OBT.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=2-00:00:00
+#SBATCH --time=3-12:00:00
 #SBATCH --job-name="mdt_contact_hist_Li-OBT"
 #SBATCH --output="mdt_contact_hist_Li-OBT_slurm-%j.out"
 #SBATCH --nodes=1
-#SBATCH --cpus-per-task=2
-#SBATCH --mem=1G
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/contact_hist_Li-OE.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=2-00:00:00
+#SBATCH --time=3-12:00:00
 #SBATCH --job-name="mdt_contact_hist_Li-OE"
 #SBATCH --output="mdt_contact_hist_Li-OE_slurm-%j.out"
 #SBATCH --nodes=1
-#SBATCH --cpus-per-task=2
-#SBATCH --mem=1G
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/contact_hist_O-Li.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=2-00:00:00
+#SBATCH --time=7-00:00:00
 #SBATCH --job-name="mdt_contact_hist_O-Li"
 #SBATCH --output="mdt_contact_hist_O-Li_slurm-%j.out"
 #SBATCH --nodes=1
-#SBATCH --cpus-per-task=2
-#SBATCH --mem=1G
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/contact_hist_OBT-Li.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=2-00:00:00
+#SBATCH --time=3-12:00:00
 #SBATCH --job-name="mdt_contact_hist_OBT-Li"
 #SBATCH --output="mdt_contact_hist_OBT-Li_slurm-%j.out"
 #SBATCH --nodes=1
-#SBATCH --cpus-per-task=2
-#SBATCH --mem=1G
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
 # The above options are only default values that can be overwritten by
 # command-line arguments
 

analysis/lintf2_ether/mdt/contact_hist_OE-Li.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=2-00:00:00
+#SBATCH --time=3-12:00:00
 #SBATCH --job-name="mdt_contact_hist_OE-Li"
 #SBATCH --output="mdt_contact_hist_OE-Li_slurm-%j.out"
 #SBATCH --nodes=1
-#SBATCH --cpus-per-task=2
-#SBATCH --mem=1G
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=512M
 # The above options are only default values that can be overwritten by
 # command-line arguments