Alphafold3

containers/alphafold3/alphafold3.def

@@ -0,0 +1,69 @@
+Bootstrap: docker
+From: nvidia/cuda:12.6.3-base-ubuntu24.04
+
+# based on https://github.com/google-deepmind/alphafold3/blob/main/docker/Dockerfile
+%labels
+    Author John LaGrone <jlagrone@smu.edu>
+    Version 1.0
+    Framework AlphaFold
+    Distribution Ubuntu 22.04
+    Application AlphaFold 3
+
+%apprun run_alphafold.py
+  exec uv run python3 /app/alphafold/run_alphafold.py --model_dir=/models --db_dir=/public_databases "${@}"
+
+%files
+  jackhmmer_seq_limit.patch
+
+%post
+  ALPHAFOLD_TAG="v3.0.4"
+  DEBIAN_FRONTEND=noninteractive \
+    apt-get update --quiet \
+    && apt-get install --yes --quiet python3.12 python3.12-dev \
+    && apt-get install --yes --quiet git wget gcc g++ make zlib1g-dev zstd curl ca-certificates
+
+  curl -LsSf https://astral.sh/uv/install.sh | sh    
+  export PATH="/root/.local/bin:$PATH"
+
+  export UV_COMPILE_BYTECODE=1
+  export UV_PROJECT_ENVIRONMENT=/alphafold3_venv
+  PATH="/hmmer/bin:/alphafold3_venv/bin:$PATH"
+
+  export PATH="/hmmer/bin:/alphafold3_venv/bin:$PATH"
+
+  mkdir /hmmer_build /hmmer ; \
+    wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz --directory-prefix /hmmer_build ; \
+    cd /hmmer_build && echo "ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 hmmer-3.4.tar.gz" | sha256sum --check && \
+    cd /hmmer_build && tar zxf hmmer-3.4.tar.gz && rm hmmer-3.4.tar.gz
+
+  cd /hmmer_build && patch -p0 < /jackhmmer_seq_limit.patch
+
+  cd /hmmer_build/hmmer-3.4 && ./configure --prefix /hmmer && \
+    cd /hmmer_build/hmmer-3.4 && make -j && \
+    cd /hmmer_build/hmmer-3.4 && make install && \
+    cd /hmmer_build/hmmer-3.4/easel && make install && \
+    rm -R /hmmer_build && \
+    cd
+
+  git clone https://github.com/google-deepmind/alphafold3.git && \
+    cd alphafold3 && \
+    git checkout ${ALPHAFOLD_TAG} && \
+    cd && \
+    mkdir -p /app && \
+    mv alphafold3 /app/alphafold && \
+    cd /app/alphafold && \
+    UV_LINK_MODE=copy uv sync --frozen --all-groups --no-editable
+
+  cd /app/alphafold && \
+    uv run build_data
+
+
+
+%environment
+  export PATH="/root/.local/bin:$PATH"
+  export UV_COMPILE_BYTECODE=1
+  export UV_PROJECT_ENVIRONMENT=/alphafold3_venv
+  export PATH="/hmmer/bin:/alphafold3_venv/bin:$PATH"
+  export XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
+  export XLA_PYTHON_CLIENT_PREALLOCATE=true
+  export XLA_CLIENT_MEM_FRACTION=0.95

containers/alphafold3/jackhmmer_seq_limit.patch

@@ -0,0 +1,32 @@
+--- hmmer-3.4/src/jackhmmer.c
++++ hmmer-3.4/src/jackhmmer.c
+@@ -73,6 +73,7 @@ static ESL_OPTIONS options[] = {
+   { "--noali",      eslARG_NONE,        FALSE, NULL, NULL,      NULL,    NULL,  NULL,            "don't output alignments, so output is smaller",                2 },
+   { "--notextw",    eslARG_NONE,         NULL, NULL, NULL,      NULL,    NULL, "--textw",        "unlimit ASCII text output line width",                         2 },
+   { "--textw",      eslARG_INT,         "120", NULL, "n>=120",  NULL,    NULL, "--notextw",      "set max width of ASCII text output lines",                     2 },
++  { "--seq_limit",  eslARG_INT,          NULL, NULL, NULL,      NULL,    NULL, "--seq_limit",    "if set, truncate all hits after this value is reached",        2 },
+ /* Control of scoring system */
+   { "--popen",      eslARG_REAL,       "0.02", NULL, "0<=x<0.5",NULL,    NULL,  NULL,            "gap open probability",                                         3 },
+   { "--pextend",    eslARG_REAL,        "0.4", NULL, "0<=x<1",  NULL,    NULL,  NULL,            "gap extend probability",                                       3 },
+@@ -298,6 +299,7 @@ output_header(FILE *ofp, ESL_GETOPTS *go
+   if (esl_opt_IsUsed(go, "--noali")      && fprintf(ofp, "# show alignments in output:       no\n")                                                   < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+   if (esl_opt_IsUsed(go, "--notextw")    && fprintf(ofp, "# max ASCII text line length:      unlimited\n")                                            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+   if (esl_opt_IsUsed(go, "--textw")      && fprintf(ofp, "# max ASCII text line length:      %d\n",             esl_opt_GetInteger(go, "--textw"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
++  if (esl_opt_IsUsed(go, "--seq_limit")  && fprintf(ofp, "# set max sequence hits to return: %d\n",             esl_opt_GetInteger(go, "--seq_limit")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+   if (esl_opt_IsUsed(go, "--popen")      && fprintf(ofp, "# gap open probability:            %f\n",             esl_opt_GetReal   (go, "--popen"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+   if (esl_opt_IsUsed(go, "--pextend")    && fprintf(ofp, "# gap extend probability:          %f\n",             esl_opt_GetReal   (go, "--pextend"))  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+   if (esl_opt_IsUsed(go, "--mx")         && fprintf(ofp, "# subst score matrix (built-in):   %s\n",             esl_opt_GetString (go, "--mx"))       < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+@@ -674,6 +676,13 @@ serial_master(ESL_GETOPTS *go, struct cf
+ 	  /* Print the results. */
+ 	  p7_tophits_SortBySortkey(info->th);
+ 	  p7_tophits_Threshold(info->th, info->pli);
++	  /* Limit the number of hits if specified. */
++	  if (esl_opt_IsOn(go, "--seq_limit"))
++	  {
++	    int seq_limit = esl_opt_GetInteger(go, "--seq_limit");
++	    info->th->N = ESL_MIN(info->th->N, seq_limit);
++	  }
++
+ 	  p7_tophits_CompareRanking(info->th, kh, &nnew_targets);
+ 	  p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+ 	  p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

modules/mp/apps/alphafold/3.0.4.lua

@@ -0,0 +1,42 @@
+whatis("AlphaFold3")
+family("alphafold")
+
+help([[Name: AlphaFold3
+Version: 3.0.4
+Website: https://github.com/google-deepmind/alphafold3
+License Owners : 
+
+AlphaFold 3 is an advanced artificial intelligence model created by Google DeepMind and Isomorphic Labs that predicts the 3D structures and interactions of all of life's major molecules, going far beyond just proteins.
+]])
+
+LmodMessage('Terms of Use:')
+LmodMessage('https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md')
+LmodMessage('') 
+LmodMessage('Usage:')
+LmodMessage("run_alphafold.py --json_path=/path/to/fold_input.json  --output_dir=/path/to/af_output")
+LmodMessage('')
+LmodMessage('Do not set the model_dir or database directory options. These are already set to minimize system load.')
+
+local jobid = os.getenv("SLURM_JOB_ID") or ""
+
+if (jobid == nil or jobid == "") then
+    LmodBreak("\nRunning AlphaFold outside of a job is not permitted. Please submit a job.\n")
+end
+
+always_load('apptainer')
+local container_path="/hpc/m3/containers/alphafold3.sif"
+local flags="--nv  -B /hpc/mp/apps/alphafold/alphafold3_models/:/models --mount type=bind,src=/raid/local/datasets/alphafold3_dbs.squashfs,dst=/public_databases,ro,image-src=/ --app"
+
+setenv("APPTAINERENV_JAX_PLATFORMS", "cuda")
+
+function build_command(app, appname)
+   local app_command = pathJoin(app_path, app)
+   local cmd        = 'apptainer run  ' .. flags .. ' ' .. appname ..  ' '  .. container_path
+   local sh_ending  = ' "$@"'
+   local csh_ending = ' $*'
+   local sh_cmd     = cmd .. sh_ending
+   local csh_cmd    = cmd .. csh_ending
+   set_shell_function(app, sh_cmd, csh_cmd)
+end
+
+build_command("run_alphafold.py", "run_alphafold.py")