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esmf: Fix build (#5607)

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- Use libs instead of lapack_libs (see #3364).
- Add a patch to fix building with recent versions of gcc.
- Add a patch to fix building with mvapich2.
This commit is contained in:
Michael Kuhn 2017-10-05 16:58:40 +02:00 committed by Christoph Junghans
parent 21c79edb10
commit fe551a4d9a
3 changed files with 266 additions and 4 deletions
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26
var/spack/repos/builtin/packages/esmf/gcc.patch Normal file
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@ -0,0 +1,26 @@
From 3706bf758012daebadef83d6575c477aeff9c89b Mon Sep 17 00:00:00 2001
From: Walter Spector <wws@sgi.com>
Date: Fri, 29 Apr 2016 12:57:16 -0700
Subject: [PATCH] Fix a file open test in the Moab I/O code that gcc 6.1
noticed.
---
src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp b/src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp
index 1c44057..89e5f23 100644
--- a/src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp
+++ b/src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp
@@ -105,7 +105,7 @@ void ReadABAQUS::reset()
ReadABAQUS::~ReadABAQUS()
{
mdbImpl->release_interface(readMeshIface);
- if (NULL != abFile)
+ if (abFile.is_open())
abFile.close();
}
--
2.7.4

225
var/spack/repos/builtin/packages/esmf/mvapich2.patch Normal file
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@ -0,0 +1,225 @@
From 34de0ccf556ba75d35c9687dae5d9f666a1b2a18 Mon Sep 17 00:00:00 2001
From: Walter Spector <wws@sgi.com>
Date: Tue, 22 Nov 2016 10:57:53 -0800
Subject: [PATCH] Detect and use libmpifort when available in mvaphich2
configurations.
---
build_config/Darwin.absoft.default/build_rules.mk | 1 +
build_config/Darwin.g95.default/build_rules.mk | 1 +
build_config/Darwin.gfortran.default/build_rules.mk | 1 +
build_config/Darwin.gfortranclang.default/build_rules.mk | 1 +
build_config/Darwin.intel.default/build_rules.mk | 1 +
build_config/Darwin.nag.default/build_rules.mk | 1 +
build_config/Linux.absoft.default/build_rules.mk | 1 +
build_config/Linux.g95.default/build_rules.mk | 1 +
build_config/Linux.gfortran.default/build_rules.mk | 1 +
build_config/Linux.gfortranclang.default/build_rules.mk | 1 +
build_config/Linux.intel.default/build_rules.mk | 1 +
build_config/Linux.intelgcc.default/build_rules.mk | 1 +
build_config/Linux.lahey.default/build_rules.mk | 1 +
build_config/Linux.nag.default/build_rules.mk | 1 +
build_config/Linux.pgi.default/build_rules.mk | 1 +
scripts/libs.mvapich2f90 | 10 ++++++++++
16 files changed, 25 insertions(+)
create mode 100755 scripts/libs.mvapich2f90
diff --git a/build_config/Darwin.absoft.default/build_rules.mk b/build_config/Darwin.absoft.default/build_rules.mk
index 059ff82..88a95fe 100644
--- a/build_config/Darwin.absoft.default/build_rules.mk
+++ b/build_config/Darwin.absoft.default/build_rules.mk
@@ -53,6 +53,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Darwin.g95.default/build_rules.mk b/build_config/Darwin.g95.default/build_rules.mk
index 9789b26..a7bf89c 100644
--- a/build_config/Darwin.g95.default/build_rules.mk
+++ b/build_config/Darwin.g95.default/build_rules.mk
@@ -54,6 +54,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Darwin.gfortran.default/build_rules.mk b/build_config/Darwin.gfortran.default/build_rules.mk
index 96a2a4f..2e05248 100644
--- a/build_config/Darwin.gfortran.default/build_rules.mk
+++ b/build_config/Darwin.gfortran.default/build_rules.mk
@@ -53,6 +53,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Darwin.gfortranclang.default/build_rules.mk b/build_config/Darwin.gfortranclang.default/build_rules.mk
index da52f08..cf90636 100644
--- a/build_config/Darwin.gfortranclang.default/build_rules.mk
+++ b/build_config/Darwin.gfortranclang.default/build_rules.mk
@@ -56,6 +56,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Darwin.intel.default/build_rules.mk b/build_config/Darwin.intel.default/build_rules.mk
index f6593f1..b851691 100644
--- a/build_config/Darwin.intel.default/build_rules.mk
+++ b/build_config/Darwin.intel.default/build_rules.mk
@@ -53,6 +53,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Darwin.nag.default/build_rules.mk b/build_config/Darwin.nag.default/build_rules.mk
index 4ee8689..1dd172d 100644
--- a/build_config/Darwin.nag.default/build_rules.mk
+++ b/build_config/Darwin.nag.default/build_rules.mk
@@ -53,6 +53,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.absoft.default/build_rules.mk b/build_config/Linux.absoft.default/build_rules.mk
index 7a2314e..43231c9 100644
--- a/build_config/Linux.absoft.default/build_rules.mk
+++ b/build_config/Linux.absoft.default/build_rules.mk
@@ -53,6 +53,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.g95.default/build_rules.mk b/build_config/Linux.g95.default/build_rules.mk
index 5f45593..5d71e59 100644
--- a/build_config/Linux.g95.default/build_rules.mk
+++ b/build_config/Linux.g95.default/build_rules.mk
@@ -54,6 +54,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.gfortran.default/build_rules.mk b/build_config/Linux.gfortran.default/build_rules.mk
index 47b55de..2954eab 100644
--- a/build_config/Linux.gfortran.default/build_rules.mk
+++ b/build_config/Linux.gfortran.default/build_rules.mk
@@ -61,6 +61,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.gfortranclang.default/build_rules.mk b/build_config/Linux.gfortranclang.default/build_rules.mk
index 4c58349..6a68841 100644
--- a/build_config/Linux.gfortranclang.default/build_rules.mk
+++ b/build_config/Linux.gfortranclang.default/build_rules.mk
@@ -64,6 +64,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.intel.default/build_rules.mk b/build_config/Linux.intel.default/build_rules.mk
index abb2873..55dd61a 100644
--- a/build_config/Linux.intel.default/build_rules.mk
+++ b/build_config/Linux.intel.default/build_rules.mk
@@ -60,6 +60,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.intelgcc.default/build_rules.mk b/build_config/Linux.intelgcc.default/build_rules.mk
index 7c0e5c9..135c822 100644
--- a/build_config/Linux.intelgcc.default/build_rules.mk
+++ b/build_config/Linux.intelgcc.default/build_rules.mk
@@ -60,6 +60,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.lahey.default/build_rules.mk b/build_config/Linux.lahey.default/build_rules.mk
index 9959bda..7a83264 100644
--- a/build_config/Linux.lahey.default/build_rules.mk
+++ b/build_config/Linux.lahey.default/build_rules.mk
@@ -57,6 +57,7 @@ ifeq ($(ESMF_COMM),mvapich2)
ESMF_F90DEFAULT = mpif90
ESMF_F90LINKERDEFAULT = mpicxx
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.nag.default/build_rules.mk b/build_config/Linux.nag.default/build_rules.mk
index 0fd6435..41a7e60 100644
--- a/build_config/Linux.nag.default/build_rules.mk
+++ b/build_config/Linux.nag.default/build_rules.mk
@@ -53,6 +53,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/build_config/Linux.pgi.default/build_rules.mk b/build_config/Linux.pgi.default/build_rules.mk
index f6380b1..052a1cb 100644
--- a/build_config/Linux.pgi.default/build_rules.mk
+++ b/build_config/Linux.pgi.default/build_rules.mk
@@ -80,6 +80,7 @@ ifeq ($(ESMF_COMM),mvapich2)
# Mvapich2 ---------------------------------------------------
ESMF_F90DEFAULT = mpif90
ESMF_CXXDEFAULT = mpicxx
+ESMF_CXXLINKLIBS += $(shell $(ESMF_DIR)/scripts/libs.mvapich2f90)
ESMF_MPIRUNDEFAULT = mpirun $(ESMF_MPILAUNCHOPTIONS)
ESMF_MPIMPMDRUNDEFAULT = mpiexec $(ESMF_MPILAUNCHOPTIONS)
else
diff --git a/scripts/libs.mvapich2f90 b/scripts/libs.mvapich2f90
new file mode 100755
index 0000000..e4b6f27
--- /dev/null
+++ b/scripts/libs.mvapich2f90
@@ -0,0 +1,10 @@
+#!/bin/sh
+# this scripts determines the correct MVAPICH2 Fortran bindings library to
+# use when mpicxx is used for linking. If libmpifort, use it.
+PATHEXE=`which mpicxx`
+MVAPICH2_LIBDIR=`dirname ${PATHEXE}`/../lib*
+ls -1 ${MVAPICH2_LIBDIR} | grep mpifort > /dev/null 2>&1
+if [ $? = 0 ]; then
+ echo -lmpifort;
+fi
+
--
2.7.4

19
var/spack/repos/builtin/packages/esmf/package.py
View file

@ -61,9 +61,20 @@ class Esmf(MakefilePackage):
# Testing dependencies
# depends_on('perl', type='test') # TODO: Add a test deptype
# NOTE: ESMF cannot be installed with GCC 6. It uses constructs that
# are no longer valid in GCC 6. GCC 4 is recommended for installation.
conflicts('%gcc@6:')
# Make esmf build with newer gcc versions
# https://sourceforge.net/p/esmf/esmf/ci/3706bf758012daebadef83d6575c477aeff9c89b/
patch('gcc.patch', when='@:7.0.99 %gcc@6:')
# Fix undefined reference errors with mvapich2
# https://sourceforge.net/p/esmf/esmf/ci/34de0ccf556ba75d35c9687dae5d9f666a1b2a18/
patch('mvapich2.patch', when='@:7.0.99')
# Make script from mvapich2.patch executable
@run_before('build')
@when('@:7.0.99')
def chmod_scripts(self):
chmod = which('chmod')
chmod('+x', 'scripts/libs.mvapich2f90')
def url_for_version(self, version):
return "http://www.earthsystemmodeling.org/esmf_releases/non_public/ESMF_{0}/esmf_{0}_src.tar.gz".format(version.underscored)
@ -167,7 +178,7 @@ def edit(self, spec, prefix):
# Specifies the linker directive needed to link the LAPACK library
# to the application.
os.environ['ESMF_LAPACK_LIBS'] = spec['lapack'].lapack_libs.link_flags # noqa
os.environ['ESMF_LAPACK_LIBS'] = spec['lapack'].libs.link_flags # noqa
else:
# Disables LAPACK-dependent code.
os.environ['ESMF_LAPACK'] = 'OFF'