NAMD 3.0 (GH200) (#125)

namd 3.0
eth-cscs · Jul 9, 2024 · 4c61a13 · 4c61a13
1 parent 2e97324
commit 4c61a13
Show file tree

Hide file tree

Showing 20 changed files with 1,498 additions and 13 deletions.
diff --git a/config.yaml b/config.yaml
@@ -133,6 +133,12 @@ uenvs:
         santis: [gh200]
         todi: [gh200]
       develop: False
+    "3.0":
+      recipes:
+        gh200: 3.0/gh200
+      deploy:
+        todi: [gh200]
+      develop: False
   netcdf-tools:
     "2024":
       recipes:

diff --git a/docs/uenv-namd.md b/docs/uenv-namd.md
@@ -12,39 +12,64 @@
 
 ## 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).
+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). The single-node build provides the following views:
+
+* `namd-single-node` (standard view, with NAMD)
+* `develop-single-node` (development view, without NAMD)
 
 ### 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
+export DEV_VIEW_NAME="develop-single-node"
+
 # Start uenv and load develop view
 uenv start <NAMD_UENV>
-uenv view develop
+uenv view ${DEV_VIEW_NAME}
 
-# cd to NAMD source directory
 cd <PATH_TO_NAMD_SOURCE>
 
+# Set variable VIEW_PATH to the view
+export DEV_VIEW_PATH=/user-environment/env/${DEV_VIEW_NAME}
+
 # Build bundled Charm++
-tar -xvf charm-7.0.0.tar && cd charm-v7.0.0
+tar -xvf charm-8.0.0.tar && cd charm-8.0.0
 ./build charm++ multicore-linux-arm8 gcc --with-production --enable-tracing -j 32
 
-# Build NAMD
-cd ..
+# Configure NAMD build for GPU
+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
+    --charm-arch multicore-linux-arm8-gcc --charm-base $PWD/charm-8.0.0 \
+    --with-tcl --tcl-prefix ${DEV_VIEW_PATH} \
+    --with-fftw --with-fftw3 --fftw-prefix ${DEV_VIEW_PATH} \
+    --cuda-gencode arch=compute_90,code=sm_90 --with-single-node-cuda --with-cuda --cuda-prefix ${DEV_VIEW_PATH}
 cd Linux-ARM64-g++.cuda && make -j 32
 
-export LD_LIBRARY_PATH=/user-environment/env/develop/lib/
+# !!! BEGIN OPTIONAL !!!
+# Configure NAMD build for CPU
+cd ..
+./config Linux-ARM64-g++ \
+    --charm-arch multicore-linux-arm8-gcc --charm-base $PWD/charm-8.0.0 \
+    --with-tcl --tcl-prefix ${DEV_VIEW_PATH} \
+    --with-fftw --with-fftw3 --fftw-prefix ${DEV_VIEW_PATH}
+cd Linux-ARM64-g++ && make -j 32
+# !!! END OPTIONAL !!!
+
+cd ..
+export LD_LIBRARY_PATH=${DEV_VIEW_PATH}/lib/
+
+# Run NAMD (GPU version)
+Linux-ARM64-g++.cuda/namd3 <NAMD_OPTIONS>
 
-# Run NAMD
-./namd3 <NAMD_OPTIONS>
+# !!! BEGIN OPTIONAL !!!
+# Run NAMD (CPU version)
+Linux-ARM64-g++/namd3 <NAMD_OPTIONS>
+# !!! END OPTIONAL !!!
 ```
 
+The optional section provides instructions on how to build a CPU-only build, should you need it (for constant pH MD simulations, for example).
+
 ## Useful Links
 
 * [NAMD Spack package]
@@ -65,3 +90,4 @@ export LD_LIBRARY_PATH=/user-environment/env/develop/lib/
 [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/3.0/gh200/compilers.yaml b/recipes/namd/3.0/gh200/compilers.yaml
@@ -0,0 +1,5 @@
+bootstrap:
+  spec: gcc@12
+gcc:
+  specs:
+  - [email protected]
diff --git a/recipes/namd/3.0/gh200/config.yaml b/recipes/namd/3.0/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: v0.22.0
+modules: True
diff --git a/recipes/namd/3.0/gh200/environments.yaml b/recipes/namd/3.0/gh200/environments.yaml
@@ -0,0 +1,17 @@
+namd-single-node:
+  compiler:
+  - toolchain: gcc
+    spec: [email protected]
+  unify: true
+  specs:
+  - [email protected]
+  - [email protected] +openmp ~mpi
+  - [email protected]
+  - charmpp@=8.0.0 backend=multicore +production +tracing
+  - namd@=3.0 +cuda cuda_arch=90 +single_node_gpu
+  views:
+    develop-single-node:
+      link: roots
+      exclude: ["namd"]
+    namd-single-node:
+      link: roots
diff --git a/recipes/namd/3.0/gh200/modules.yaml b/recipes/namd/3.0/gh200/modules.yaml
@@ -0,0 +1,25 @@
+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}'
+        namd+single_node_gpu: '{name}-single-node/{version}'
+        fftw~mpi: '{name}-no-mpi/{version}'
+        charmpp backend=multicore: '{name}-multicore/{version}'
+        charmpp backend=ofi : '{name}-ofi/{version}'
diff --git a/recipes/namd/3.0/gh200/pre-install b/recipes/namd/3.0/gh200/pre-install
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -u
+
+namd_version=3.0
+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/${namd}
+
+
diff --git a/recipes/namd/3.0/gh200/repo/packages/charmpp/charm_6.7.1_aocc.patch b/recipes/namd/3.0/gh200/repo/packages/charmpp/charm_6.7.1_aocc.patch
@@ -0,0 +1,188 @@
+diff -bur charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh updated-charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh
+--- charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh	2016-11-07 20:14:26.000000000 +0530
++++ updated-charm-6.7.1/src/arch/mpi-linux-x86_64/cc-mpicxx.sh	2019-08-26 16:55:40.868903291 +0530
+@@ -14,7 +14,7 @@
+
+ CMK_REAL_COMPILER=`$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