Add raw mol2/bhff dataset and bm2_long

UoB-HPC · Jul 29, 2021 · 8f215c3 · 8f215c3
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diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,5 @@ energies.dat
 *.bak
 *.ori
 *.old
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+.vscode
diff --git a/README.md b/README.md
@@ -39,7 +39,8 @@ Refer to each implementation's README for further run instructions.
 Two input decks are included in this repository:
 
 * `bm1` is a short benchmark (~100 ms/iteration on a 64-core ThunderX2 node) based on a small ligand (26 atoms)
-* `bm2` is a long benchmark (~25 s/iteration on a 64-core ThunderX2 node) based on a big ligand (2672 atoms)
+* `bm2` is a long benchmark (~25 s/iteration on a 64-core ThunderX2 node) based on a big ligand (2672 atoms)* `bm2` is a long benchmark (~25 s/iteration on a 64-core ThunderX2 node) based on a big ligand (2672 atoms)
+* `bm2_long` is a very long benchmark based on `bm2` but with 1048576 poses instead of 65536
 
 They are located in the [`data`](data/) directory, and `bm1` is run by default.
 All implementations accept a `--deck` parameter to specify an input deck directory.

diff --git a/data/bm2_long/forcefield.in b/data/bm2_long/forcefield.in
diff --git a/data/bm2_long/ligand.in b/data/bm2_long/ligand.in
diff --git a/data/bm2_long/params.txt b/data/bm2_long/params.txt
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+-f /home/tom/Desktop/bude/bude-1.2.10-release/BUDE-1.2.10/inputData/heavy_by-atom_2016-v1.bhff -p /home/tom/Desktop/bude/bude-1.2.10-release/example/virtual_screen/1GCZ/inputs/bude_1gcz_proA.mol2 -l /home/tom/Desktop/bude/bude-1.2.10-release/example/virtual_screen/1GCZ/inputs/bude_1gcz_proA.mol2 -o output -n 1048576 --force 
diff --git a/data/bm2_long/poses.in b/data/bm2_long/poses.in
diff --git a/data/bm2_long/protein.in b/data/bm2_long/protein.in
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     *.bak
     *.ori
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		-f /home/tom/Desktop/bude/bude-1.2.10-release/BUDE-1.2.10/inputData/heavy_by-atom_2016-v1.bhff -p /home/tom/Desktop/bude/bude-1.2.10-release/example/virtual_screen/1GCZ/inputs/bude_1gcz_proA.mol2 -l /home/tom/Desktop/bude/bude-1.2.10-release/example/virtual_screen/1GCZ/inputs/bude_1gcz_proA.mol2 -o output -n 1048576 --force