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Wed, 24 Aug 2022 20:32:28 GMT (envelope-from git) Date: Wed, 24 Aug 2022 20:32:28 GMT Message-Id: <202208242032.27OKWSli067787@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 0b9278ec684a - main - science/cardioid: New port: Cardiac simulation toolkit List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0b9278ec684ab7923315214fec4171e97e7a021f Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=0b9278ec684ab7923315214fec4171e97e7a021f commit 0b9278ec684ab7923315214fec4171e97e7a021f Author: Yuri Victorovich AuthorDate: 2022-08-24 20:31:19 +0000 Commit: Yuri Victorovich CommitDate: 2022-08-24 20:32:26 +0000 science/cardioid: New port: Cardiac simulation toolkit --- science/Makefile | 1 + science/cardioid/Makefile | 52 ++++++++++++++++++++++ science/cardioid/distinfo | 5 +++ .../cardioid/files/patch-simUtil_src_ddcMalloc.c | 20 +++++++++ .../cardioid/files/patch-simUtil_src_utilities.c | 22 +++++++++ science/cardioid/pkg-descr | 6 +++ 6 files changed, 106 insertions(+) diff --git a/science/Makefile b/science/Makefile index dc6dd9d62a78..75361ae656a0 100644 --- a/science/Makefile +++ b/science/Makefile @@ -38,6 +38,7 @@ SUBDIR += bodr SUBDIR += buddy SUBDIR += cantera + SUBDIR += cardioid SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk diff --git a/science/cardioid/Makefile b/science/cardioid/Makefile new file mode 100644 index 000000000000..d60938ab7143 --- /dev/null +++ b/science/cardioid/Makefile @@ -0,0 +1,52 @@ +PORTNAME= cardioid +PORTVERSION= g20211026 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Cardiac simulation toolkit + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libblas.so:math/blas \ + liblapack.so:math/lapack +RUN_DEPENDS= bash:shells/bash + +USES= cmake:testing compiler:c++11-lang shebangfix + +USE_GITHUB= yes +GH_ACCOUNT= LLNL +GH_TAGNAME= 2f66d9f +GH_TUPLE= mfem:mfem:v4.4:mfem + +SHEBANG_FILES= elec/compileReaction.template + +CMAKE_TESTING_ON= ENABLE_TESTS + +PLIST_FILES= bin/cardioid \ + bin/compileReaction \ + bin/singleCell + +OPTIONS_DEFINE= MFEM OPENMP +OPTIONS_SINGLE= MFEM MPI +OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI +OPTIONS_DEFAULT= MPICH OPENMP +OPTIONS_SUB= yes + +MFEM_DESC= Build with MFEM mesh library +MFEM_CMAKE_ON= -DMFEM_DIR=${WRKSRC_mfem} +MFEM_BROKEN= see https://github.com/LLNL/cardioid/issues/15 + +NOMPI_DESC= Build without parallel processing support +NOMPI_BROKEN= https://github.com/LLNL/axom/issues/913 + +MPICH_USES= mpi:mpich +MPICH_CMAKE_ON= -DENABLE_MPI=ON + +OPENMPI_USES= mpi:openmpi +OPENMPI_CMAKE_ON= -DENABLE_MPI=ON + +OPENMP_CMAKE_BOOL= ENABLE_OPENMP +OPENMP_BROKEN_OFF= https://github.com/LLNL/cardioid/issues/14 + +.include diff --git a/science/cardioid/distinfo b/science/cardioid/distinfo new file mode 100644 index 000000000000..e951f8b0b77c --- /dev/null +++ b/science/cardioid/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1661371882 +SHA256 (LLNL-cardioid-g20211026-2f66d9f_GH0.tar.gz) = 16bfedb27110170adcf8f3090379a56c8e1637256e2761e85d98c9c043dcf970 +SIZE (LLNL-cardioid-g20211026-2f66d9f_GH0.tar.gz) = 6781832 +SHA256 (mfem-mfem-v4.4_GH0.tar.gz) = 0325a57854d9268dfe3f8d9b03836eb01b00a966d93162e6249857e9fab9c61f +SIZE (mfem-mfem-v4.4_GH0.tar.gz) = 3078651 diff --git a/science/cardioid/files/patch-simUtil_src_ddcMalloc.c b/science/cardioid/files/patch-simUtil_src_ddcMalloc.c new file mode 100644 index 000000000000..1fe7184b1200 --- /dev/null +++ b/science/cardioid/files/patch-simUtil_src_ddcMalloc.c @@ -0,0 +1,20 @@ +--- simUtil/src/ddcMalloc.c.orig 2022-08-24 19:49:58 UTC ++++ simUtil/src/ddcMalloc.c +@@ -381,6 +381,8 @@ void printHeapInfo(FILE* file) + { + #ifdef __APPLE__ + fprintf(file, "In routine printHeapInfo no mallinfo on OS X. Sorry.\n"); ++#elif defined(__FreeBSD__) ++ fprintf(file, "In routine printHeapInfo no mallinfo on FreeBSD. Sorry.\n"); + #else + struct mallinfo minfo; + minfo = mallinfo(); +@@ -397,6 +399,8 @@ void printHeapInfo_pio(PFILE* file) + { + #ifdef __APPLE__ + Pprintf(file, "No mallinfo on OS X. Sorry.\n"); ++#elif defined(__FreeBSD__) ++ Pprintf(file, "No mallinfo on FreeBSD. Sorry.\n"); + #else + struct mallinfo minfo; + minfo = mallinfo(); diff --git a/science/cardioid/files/patch-simUtil_src_utilities.c b/science/cardioid/files/patch-simUtil_src_utilities.c new file mode 100644 index 000000000000..7f058e25dbce --- /dev/null +++ b/science/cardioid/files/patch-simUtil_src_utilities.c @@ -0,0 +1,22 @@ +--- simUtil/src/utilities.c.orig 2022-08-24 19:51:03 UTC ++++ simUtil/src/utilities.c +@@ -72,6 +72,10 @@ void mem_debug(char *mem_str) + static int flag =1; + if (flag) printf("No mallinfo on OS X. Sorry no minfo for <%s>.\n",mem_str); + flag =0; ++#elif defined(__FreeBSD__) ++ static int flag =1; ++ if (flag) printf("No mallinfo on FreeBSD. Sorry no minfo for <%s>.\n",mem_str); ++ flag =0; + #else + static struct mallinfo old_minfo, minfo; + static int gstep = 0; +@@ -98,7 +102,7 @@ void mem_debug(char *mem_str) + */ + void CHKMEM(char *string) + { +-#ifndef __APPLE__ ++#if !defined(__APPLE__) && !defined(__FreeBSD__) + #include + static struct mallinfo minfo, minfosave; + minfosave = minfo; diff --git a/science/cardioid/pkg-descr b/science/cardioid/pkg-descr new file mode 100644 index 000000000000..d8361d2e9d39 --- /dev/null +++ b/science/cardioid/pkg-descr @@ -0,0 +1,6 @@ +Cardioid is a cardiac multiscale simulation suite spanning from subcellular +mechanisms up to simulations of organ-level clinical phenomena. The suite +contains tools for simulating cardiac electrophysiology, cardiac mechanics, +torso-ECGs, cardiac meshing and fiber generation tools. + +WWW: https://github.com/LLNL/cardioid