NAMD 3.0b6 (GH200, single node) (#85)

The `charmpp` and `namd` packages include the following PRs (not yet included in a release of Spack): * spack/spack#42979 * spack/spack#43215 * spack/spack#43191
eth-cscs · May 22, 2024 · f6b135c · f6b135c
1 parent 76f43a0
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diff --git a/config.yaml b/config.yaml
@@ -100,6 +100,13 @@ uenvs:
       deploy:
         clariden: [a100]
       develop: False
+  namd:
+    "3.0b6":
+      recipes:
+        gh200: 3.0b6/gh200
+      deploy:
+        santis: [gh200]
+      develop: False
   netcdf-tools:
     "2024":
       recipes:

diff --git a/docs/uenv-namd.md b/docs/uenv-namd.md
@@ -0,0 +1,67 @@
+# NAMD
+
+[NAMD] is a parallel molecular dynamics code based on [Charm++] designed for high-performance simulation of large biomolecular systems.
+
+!!! danger "Licensing Terms and Conditions"
+
+    [NAMD] is distributed free of charge for research purposes only and not for commercial use: users must agree to [NAMD license] in order to use it at [CSCS]. Users agree to acknowledge use of [NAMD] in any reports or publications of results obtained with the Software (see [NAMD Homepage] for details).
+
+!!! warning
+
+    Currently, we only provide single-GPU and single-node multi-GPU [NAMD] builds, which greatly benefit from the new GPU-resident mode providing very fast dynamics (see [NAME 3.0 new features]). If you require a multi-node version of [NAMD], please contact us.
+
+## Single-node build
+
+The single-node build works on a single node and benefits from the new GPU-resident mode (see [NAMD 3.0b6 GPU-Resident benchmarking results] for more details).
+
+### Building from source
+
+The [NAMD] `uenv` provides all the dependencies required to build [NAMD] from source. You can follow these steps to build [NAMD] from source:
+
+```bash
+# Start uenv and load develop view
+uenv start namd.squashfs
+uenv view develop
+
+# cd to NAMD source directory
+cd <PATH_TO_NAMD_SOURCE>
+
+# Build bundled Charm++
+tar -xvf charm-7.0.0.tar && cd charm-v7.0.0
+./build charm++ multicore-linux-arm8 gcc --with-production --enable-tracing -j 32
+
+# Build NAMD
+cd ..
+./config Linux-ARM64-g++.cuda \
+    --charm-arch multicore-linux-arm8-gcc --charm-base $PWD/charm-v7.0.0 \
+    --with-tcl --tcl-prefix /user-environment/env/develop \
+    --with-fftw --with-fftw3 --fftw-prefix /user-environment/env/develop \
+    --cuda-gencode arch=compute_90,code=sm_90 --with-single-node-cuda --with-cuda --cuda-prefix /user-environment/env/develop
+cd Linux-ARM64-g++.cuda && make -j 32
+
+export LD_LIBRARY_PATH=/user-environment/env/develop/lib/
+
+# Run NAMD
+./namd3 <NAMD_OPTIONS>
+```
+
+## Useful Links
+
+* [NAMD Spack package]
+* [NAMD Tutorials]
+* [Charm++ Spack package]
+* [Running Charm++ Programs]
+* [What you should know about NAMD and Charm++ but were hoping to ignore] by J. C. Phillips
+
+[Charm++]: https://charm.cs.uiuc.edu/ 
+[Charm++ Spack package]: https://packages.spack.io/package.html?name=charmpp 
+[CSCS]: https://www.cscs.ch
+[NAMD]: http://www.ks.uiuc.edu/Research/namd/
+[NAMD Homepage]: http://www.ks.uiuc.edu/Research/namd/
+[NAMD license]: http://www.ks.uiuc.edu/Research/namd/license.html
+[NAMD Tutorials]: http://www.ks.uiuc.edu/Training/Tutorials/index.html#namd
+[NAMD Spack package]: https://packages.spack.io/package.html?name=namd
+[Running Charm++ Programs]: https://charm.readthedocs.io/en/latest/charm++/manual.html#running-charm-programs
+[What you should know about NAMD and Charm++ but were hoping to ignore]: https://dl.acm.org/doi/pdf/10.1145/3219104.3219134
+[NAMD 3.0 new features]: https://www.ks.uiuc.edu/Research/namd/3.0/features.html
+[NAMD 3.0b6 GPU-Resident benchmarking results]: https://www.ks.uiuc.edu/Research/namd/benchmarks/
diff --git a/recipes/namd/3.0b6/gh200/compilers.yaml b/recipes/namd/3.0b6/gh200/compilers.yaml
@@ -0,0 +1,5 @@
+bootstrap:
+  spec: gcc@12
+gcc:
+  specs:
+  - [email protected]
diff --git a/recipes/namd/3.0b6/gh200/config.yaml b/recipes/namd/3.0b6/gh200/config.yaml
@@ -0,0 +1,7 @@
+name: namd
+description: "NAMD: Scalable Molecular Dynamics" 
+store: /user-environment
+spack:
+  repo: https://github.com/spack/spack.git
+  commit: v0.21.2
+modules: True
diff --git a/recipes/namd/3.0b6/gh200/environments.yaml b/recipes/namd/3.0b6/gh200/environments.yaml
@@ -0,0 +1,17 @@
+namd-single-node:
+  compiler:
+  - toolchain: gcc
+    spec: [email protected]
+  unify: true
+  specs:
+  - cuda@12
+  - [email protected] +openmp ~mpi
+  - [email protected]
+  - charmpp@7 backend=multicore +production +tracing
+  - [email protected] +cuda cuda_arch=90 +single_node_gpu
+  views:
+    develop:
+      link: roots
+      exclude: ["namd"]
+    namd:
+      link: roots
diff --git a/recipes/namd/3.0b6/gh200/modules.yaml b/recipes/namd/3.0b6/gh200/modules.yaml
@@ -0,0 +1,21 @@
+modules:
+  prefix_inspections:
+    bin:
+      - PATH
+    lib:
+      - LD_LIBRARY_PATH
+    lib64:
+      - LD_LIBRARY_PATH
+
+  default:
+    arch_folder: false
+    roots:
+      tcl: /user-environment/modules
+    tcl:
+      all:
+        autoload: none
+      hash_length: 0
+      exclude_implicits: true
+      exclude: ['%[email protected]', 'gcc %[email protected]']
+      projections:
+        all: '{name}/{version}'
diff --git a/recipes/namd/3.0b6/gh200/pre-install b/recipes/namd/3.0b6/gh200/pre-install
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+set -u
+
+namd_version=3.0b6
+namd=NAMD_${namd_version}_Source.tar.gz 
+
+username=$CSCS_REGISTRY_USERNAME
+password=$CSCS_REGISTRY_PASSWORD
+
+curl -u ${username}:${password} https://jfrog.svc.cscs.ch/artifactory/uenv-sources/namd/${namd} --output {{ env.build }}/environments/${namd}
+
+sha256sum {{ env.build }}/environments/${namd}
diff --git a/recipes/namd/3.0b6/gh200/repo/packages/charmpp/charm_6.7.1_aocc.patch b/recipes/namd/3.0b6/gh200/repo/packages/charmpp/charm_6.7.1_aocc.patch
@@ -0,0 +1,188 @@
+diff -bur charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh updated-charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh
+--- charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh	2016-11-07 20:14:26.000000000 +0530
++++ updated-charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh	2019-08-26 16:55:40.868903291 +0530
+@@ -14,7 +14,7 @@
+
+ CMK_REAL_COMPILER=`$MPICXX -show 2>/dev/null | cut -d' ' -f1 `
+ case "$CMK_REAL_COMPILER" in
+-g++)   CMK_AMD64="-m64 -fPIC" ;;
++clang++)   CMK_AMD64="-m64 -fPIC" ;;
+ icpc)  CMK_AMD64="-m64";;
+ pgCC)  CMK_AMD64="-DCMK_FIND_FIRST_OF_PREDICATE=1 --no_using_std " ;;
+ FCC)   CMK_AMD64="-Kfast -DCMK_FIND_FIRST_OF_PREDICATE=1 --variadic_macros";;
+diff -bur charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach-scyld.sh updated-charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach-scyld.sh
+--- charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach-scyld.sh	2016-11-07 20:14:26.000000000 +0530
++++ updated-charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach-scyld.sh	2019-08-26 16:55:40.868903291 +0530
+@@ -1,14 +1,14 @@
+
+ case "$CMK_CC" in
+ mpicc*)
+-	CMK_CPP_C="gcc -E "
+-	CMK_CC="gcc -fPIC"
+-	CMK_CC_RELIABLE="gcc  -fPIC"
+-	CMK_CC_FASTEST="gcc  -fPIC"
+-	CMK_CXX="g++ -fPIC"
+-	CMK_CXXPP="gcc -E "
+-	CMK_LD="gcc"
+-	CMK_LDXX="g++"
++	CMK_CPP_C="clang -E "
++	CMK_CC="clang -fPIC"
++	CMK_CC_RELIABLE="clang  -fPIC"
++	CMK_CC_FASTEST="clang  -fPIC"
++	CMK_CXX="clang++ -fPIC"
++	CMK_CXXPP="clang -E "
++	CMK_LD="clang"
++	CMK_LDXX="clang++"
+
+ # native compiler for compiling charmxi, etc
+ 	CMK_NATIVE_CC="$CMK_CC"
+Only in updated-charm-6.7.1/src/arch/mpi-linux-x86_64: conv-mach-scyld.sh.orig
+Only in updated-charm-6.7.1/src/arch/mpi-linux-x86_64: conv-mach-scyld.sh.rej
+diff -bur charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach.sh updated-charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach.sh
+--- charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach.sh	2016-11-07 20:14:26.000000000 +0530
++++ updated-charm-6.7.1/src/arch/mpi-linux-x86_64/conv-mach.sh	2019-08-26 16:55:40.868903291 +0530
+@@ -23,7 +23,7 @@
+
+ CMK_REAL_COMPILER=`$MPICXX -show 2>/dev/null | cut -d' ' -f1 `
+ case "$CMK_REAL_COMPILER" in
+-g++) CMK_AMD64_CC="$CMK_GCC64"; CMK_AMD64_CXX="$CMK_GCC64" ;;
++clang++) CMK_AMD64_CC="$CMK_GCC64"; CMK_AMD64_CXX="$CMK_GCC64" ;;
+ pgCC)  CMK_AMD64_CC="-fPIC"; CMK_AMD64_CXX="-fPIC -DCMK_FIND_FIRST_OF_PREDICATE=1 --no_using_std " ;;
+ charmc)  echo "Error> charmc can not call AMPI's mpicxx/mpiCC wrapper! Please fix your PATH."; exit 1 ;;
+ esac
+@@ -38,10 +38,10 @@
+ CMK_LIBS="-lckqt $CMK_SYSLIBS "
+ CMK_LD_LIBRARY_PATH="-Wl,-rpath,$CHARMLIBSO/"
+
+-CMK_NATIVE_CC="gcc $CMK_GCC64 "
+-CMK_NATIVE_LD="gcc $CMK_GCC64 "
+-CMK_NATIVE_CXX="g++ $CMK_GCC64 "
+-CMK_NATIVE_LDXX="g++ $CMK_GCC64 "
++CMK_NATIVE_CC="clang $CMK_GCC64 "
++CMK_NATIVE_LD="clang $CMK_GCC64 "
++CMK_NATIVE_CXX="clang++ $CMK_GCC64 "
++CMK_NATIVE_LDXX="clang++ $CMK_GCC64 "
+ CMK_NATIVE_LIBS=""
+
+ # fortran compiler 
+@@ -51,7 +51,7 @@
+ #    CMK_FPP="/lib/cpp -P -CC"
+ #    CMK_CF90="$CMK_CF90 -fpic -fautomatic -fdollar-ok "
+ #    CMK_CF90_FIXED="$CMK_CF90 -ffixed-form "
+-#    CMK_F90LIBS="-lgfortran "
++#    CMK_F90LIBS="  "
+ #    CMK_F90_USE_MODDIR=1
+ #    CMK_F90_MODINC="-I"
+ #    CMK_MOD_NAME_ALLCAPS=
+diff -bur charm-6.7.1/src/libs/ck-libs/ckloop/Makefile updated-charm-6.7.1/src/libs/ck-libs/ckloop/Makefile
+--- charm-6.7.1/src/libs/ck-libs/ckloop/Makefile	2016-11-07 20:14:28.000000000 +0530
++++ updated-charm-6.7.1/src/libs/ck-libs/ckloop/Makefile	2019-08-26 16:55:40.852903122 +0530
+@@ -38,7 +38,7 @@
+         for i in $(LIBOBJ) ; do \
+ 	      SRCFILE=`basename $$i .o`.C ; \
+               echo "checking dependencies for $$i : $$SRCFILE" ; \
+-              g++ -MM -Wno-deprecated -I$(CDIR)/tmp $$SRCFILE >> $(DEPENDFILE); \
++              clang++ -MM -Wno-deprecated -I$(CDIR)/tmp $$SRCFILE >> $(DEPENDFILE); \
+               echo '	$$(CHARMC) -I$(CDIR)/tmp -o '$$i $$SRCFILE >> $(DEPENDFILE) ; \
+         done; 
+
+Only in updated-charm-6.7.1/src/libs/ck-libs/ckloop: Makefile.orig
+Only in updated-charm-6.7.1/src/libs/ck-libs/ckloop: Makefile.rej
+diff -bur charm-6.7.1/src/libs/ck-libs/completion/Makefile updated-charm-6.7.1/src/libs/ck-libs/completion/Makefile
+--- charm-6.7.1/src/libs/ck-libs/completion/Makefile	2016-11-07 20:14:28.000000000 +0530
++++ updated-charm-6.7.1/src/libs/ck-libs/completion/Makefile	2019-08-26 16:55:40.852903122 +0530
+@@ -45,7 +45,7 @@
+         for i in $(LIBOBJ) ; do \
+ 	      SRCFILE=`basename $$i .o`.C ; \
+               echo "checking dependencies for $$i : $$SRCFILE" ; \
+-              g++ -MM -Wno-deprecated -I$(CDIR)/tmp $$SRCFILE >> $(DEPENDFILE); \
++              clang++ -MM -Wno-deprecated -I$(CDIR)/tmp $$SRCFILE >> $(DEPENDFILE); \
+               echo '	$$(CHARMC) -I$(CDIR)/tmp -o '$$i $$SRCFILE >> $(DEPENDFILE) ; \
+         done; 
+
+Only in updated-charm-6.7.1/src/libs/ck-libs/completion: Makefile.orig
+Only in updated-charm-6.7.1/src/libs/ck-libs/completion: Makefile.rej
+diff -bur charm-6.7.1/src/libs/ck-libs/multicast/Makefile updated-charm-6.7.1/src/libs/ck-libs/multicast/Makefile
+--- charm-6.7.1/src/libs/ck-libs/multicast/Makefile	2016-11-07 20:14:29.000000000 +0530
++++ updated-charm-6.7.1/src/libs/ck-libs/multicast/Makefile	2019-08-26 16:55:40.852903122 +0530
+@@ -53,7 +53,7 @@
+         for i in $(LIBOBJ) ; do \
+ 	      SRCFILE=`basename $$i .o`.C ; \
+               echo "checking dependencies for $$i : $$SRCFILE" ; \
+-              g++ -MM -Wno-deprecated -I$(CDIR)/tmp $$SRCFILE >> $(DEPENDFILE); \
++              clang++ -MM -Wno-deprecated -I$(CDIR)/tmp $$SRCFILE >> $(DEPENDFILE); \
+               echo '	$$(CHARMC) -I$(CDIR)/tmp -o '$$i $$SRCFILE >> $(DEPENDFILE) ; \
+         done; 
+
+Only in updated-charm-6.7.1/src/libs/ck-libs/multicast: Makefile.orig
+Only in updated-charm-6.7.1/src/libs/ck-libs/multicast: Makefile.rej
+diff -bur charm-6.7.1/src/libs/ck-libs/NDMeshStreamer/Makefile updated-charm-6.7.1/src/libs/ck-libs/NDMeshStreamer/Makefile
+--- charm-6.7.1/src/libs/ck-libs/NDMeshStreamer/Makefile	2016-11-07 20:14:27.000000000 +0530
++++ updated-charm-6.7.1/src/libs/ck-libs/NDMeshStreamer/Makefile	2019-08-26 16:55:40.852903122 +0530
+@@ -52,7 +52,7 @@
+         for i in $(LIBOBJ) ; do \
+ 	      SRCFILE=`basename $$i .o`.C ; \
+               echo "checking dependencies for $$i : $$SRCFILE" ; \
+-              g++ -MM -Wno-deprecated -I$(CDIR)/tmp -I../completion $$SRCFILE >> $(DEPENDFILE); \
++              clang++ -MM -Wno-deprecated -I$(CDIR)/tmp -I../completion $$SRCFILE >> $(DEPENDFILE); \
+               echo '	$$(CHARMC) -I$(CDIR)/tmp -o '$$i $$SRCFILE >> $(DEPENDFILE) ; \
+         done;
+
+Only in updated-charm-6.7.1/src/libs/ck-libs/NDMeshStreamer: Makefile.orig
+Only in updated-charm-6.7.1/src/libs/ck-libs/NDMeshStreamer: Makefile.rej
+diff -bur charm-6.7.1/src/QuickThreads/Makefile updated-charm-6.7.1/src/QuickThreads/Makefile
+--- charm-6.7.1/src/QuickThreads/Makefile	2016-11-07 20:14:25.000000000 +0530
++++ updated-charm-6.7.1/src/QuickThreads/Makefile	2019-08-26 16:55:40.856903165 +0530
+@@ -1,5 +1,5 @@
+
+-CC=gcc -I. -O2
++CC=clang -I. -O2
+
+ all: qt stp testpgm
+
+diff -bur charm-6.7.1/src/scripts/Makefile updated-charm-6.7.1/src/scripts/Makefile
+--- charm-6.7.1/src/scripts/Makefile	2016-11-07 20:14:29.000000000 +0530
++++ updated-charm-6.7.1/src/scripts/Makefile	2019-08-26 16:55:40.840902996 +0530
+@@ -942,7 +942,7 @@
+ 	      SRCFILE=`basename $$i .o`.C ; \
+ 	      [ ! -f $$SRCFILE ] && SRCFILE=`basename $$i .o`.c ;	\
+               echo "checking dependencies for $$SRCFILE" ; \
+-              if g++ -MM -Wno-deprecated -I. -I$(INC) $$SRCFILE  >> $(DEPENDFILE); then true ; else echo '' ; echo "Compilation of '$$SRCFILE' failed, please fix it first!!!!" ; exit; fi;  \
++              if clang++ -MM -Wno-deprecated -I. -I$(INC) $$SRCFILE  >> $(DEPENDFILE); then true ; else echo '' ; echo "Compilation of '$$SRCFILE' failed, please fix it first!!!!" ; exit; fi;  \
+ 	      echo '' >> $(DEPENDFILE) ; \
+         done;  \
+
+@@ -968,7 +968,7 @@
+ 	      found=`/usr/bin/find $$SRCDIR -depth 1 -name $$SRCFILE`; \
+               [ ! $$found ] && SRCFILE=`basename $$i .o`.c ; \
+               echo "checking dependencies for $$SRCFILE" ; \
+-              if g++ -MM -Wno-deprecated -I. -I$(INC) $$SRCFILE  >> $(DEPENDFILE); then true ; else echo '' ; echo "Compilation of '$$SRCFILE' failed, please fix it first!!!!" ; exit; fi;  \
++              if clang++ -MM -Wno-deprecated -I. -I$(INC) $$SRCFILE  >> $(DEPENDFILE); then true ; else echo '' ; echo "Compilation of '$$SRCFILE' failed, please fix it first!!!!" ; exit; fi;  \
+ 	      echo '' >> $(DEPENDFILE) ; \
+         done;  \
+
+diff -bur charm-6.7.1/tests/charm++/megatest/Makefile updated-charm-6.7.1/tests/charm++/megatest/Makefile
+--- charm-6.7.1/tests/charm++/megatest/Makefile	2016-11-07 20:14:30.000000000 +0530
++++ updated-charm-6.7.1/tests/charm++/megatest/Makefile	2019-08-26 16:55:40.820902785 +0530
+@@ -118,7 +118,7 @@
+         for i in $(OBJS) ; do \
+               SRCFILE=`basename $$i .o`.C ; \
+               echo "checking dependencies for $$SRCFILE" ; \
+-              g++ -MM -I$(CHARMINC) $$SRCFILE | \
++              clang++ -MM -I$(CHARMINC) $$SRCFILE | \
+               perl $(CHARMBIN)/dep.pl $(CHARMINC) /usr/include /usr/local >> $(DEPENDFILE); \
+               echo '	$$(CHARMC) -o '$$i $$SRCFILE >> $(DEPENDFILE) ; \
+         done;
+--- charm-6.7.1/src/scripts/configure	2016-11-07 20:14:31.000000000 +0530
++++ updated-charm/charm-6.7.1/src/scripts/configure	2020-10-21 12:54:06.476958828 +0530
+@@ -2141,8 +2141,8 @@
+ $as_echo_n "checking \"$1\"... " >&6; }
+ 	echo "### $1" >> $charmout
+ 	cat $t >> $charmout
+-	echo $CMK_CXX -I../include -I. $CMK_LIBDIR $CMK_INCDIR $CMK_SYSINC $OPTS_CXX $OPTS_LD -c $t -o test.o $4 >> $charmout
+-	$CMK_CXX -I../include -I. $CMK_LIBDIR $CMK_INCDIR $CMK_SYSINC $OPTS_CXX $OPTS_LD -c $t -o test.o $4 > out 2>&1
++	echo $CMK_CXX -I../include -I. $CMK_LIBDIR $CMK_INCDIR $CMK_SYSINC $OPTS_CXX $OPTS_LD -Qunused-arguments -c $t -o test.o $4 >> $charmout
++	$CMK_CXX -I../include -I. $CMK_LIBDIR $CMK_INCDIR $CMK_SYSINC $OPTS_CXX $OPTS_LD -Qunused-arguments  -c $t -o test.o $4 > out 2>&1
+ 	test_result $? "$1" "$2" "$3"
+  	strictpass=$pass
+ 	strictfail=$fail