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Fwd: [Branch ~dorsal-core/dorsal/main] Rev 749: Add package for HDF5

To: dorsal <dorsal@xxxxxxxxxxxxxxxxxxx>
From: "Garth N. Wells" <gnw20@xxxxxxxxx>
Date: Sun, 21 Oct 2012 16:59:40 +0100
In-reply-to: <20121021154517.12042.31116.launchpad@ackee.canonical.com>

'parallel' should be enabled for HDF5.

Garth


---------- Forwarded message ----------
From:  <noreply@xxxxxxxxxxxxx>
Date: Sun, Oct 21, 2012 at 4:45 PM
Subject: [Branch ~dorsal-core/dorsal/main] Rev 749: Add package for HDF5
To: Garth Wells <gnw20@xxxxxxxxx>


------------------------------------------------------------
revno: 749
committer: Anders Logg <logg@glaurung>
branch nick: dorsal
timestamp: Sun 2012-10-21 08:44:12 -0700
message:
  Add package for HDF5
added:
  FEniCS/packages/hdf5.package
modified:
  FEniCS/packages/mpfr.package
  FEniCS/platforms/contributed/precise-hpc.platform
  dorsal.sh


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=== added file 'FEniCS/packages/hdf5.package'
--- FEniCS/packages/hdf5.package        1970-01-01 00:00:00 +0000
+++ FEniCS/packages/hdf5.package        2012-10-21 15:44:12 +0000
@@ -0,0 +1,22 @@
+NAME=hdf5-1.8.9
+SOURCE=http://www.hdfgroup.org/ftp/HDF5/current/src/
+PACKING=.tar.bz2
+BUILDCHAIN=custom
+
+package_specific_build () {
+
+    # Download and apply patch
+    if [ ! -e cmake_patch.txt ]
+    then
+        wget http://www.hdfgroup.org/ftp/HDF5/current/src/cmake_patch.txt
+        patch -N -Z -p0 < cmake_patch.txt
+    fi
+
+    # Configure and build
+    mkdir -p dorsal_build_dir
+    cd dorsal_build_dir
+    cmake ${CONFOPTS} -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} ..
+    make ${MAKEOPTS} -j ${PROCS}
+    make install
+
+}

=== modified file 'FEniCS/packages/mpfr.package'
--- FEniCS/packages/mpfr.package        2012-05-29 08:10:52 +0000
+++ FEniCS/packages/mpfr.package        2012-10-21 15:44:12 +0000
@@ -8,7 +8,7 @@
     if [ ! -e patches ]
     then
        wget http://www.mpfr.org/mpfr-2.2.0/patches
-    fi
+    fi
     patch -N -Z -p1 < patches
     ./configure --prefix=${INSTALL_PATH} --enable-shared=yes
     make -j ${PROCS}

=== modified file 'FEniCS/platforms/contributed/precise-hpc.platform'
--- FEniCS/platforms/contributed/precise-hpc.platform   2012-10-21
15:19:41 +0000
+++ FEniCS/platforms/contributed/precise-hpc.platform   2012-10-21
15:44:12 +0000
@@ -69,25 +69,28 @@
 echo
 read -p "Press any key to continue"

-#- Most important is ATLAS for BLAS (if MKL is not available)
-#   CHECK: added atlas.package
-#- Build LAPACK to use ATLAS BLAS
-#   CHECK: handled as part of ATLAS build
-#- Build latest OpenMPI with support for threads turned on. MPICH2
-#  works fine too
-#   CHECK: using existing openmpi.package
-#- Build Boost so that Boost.MPI uses the manually installed MPI
-#   CHECK: using existing boost.package, did it detect MPI???
-#- Install CGAL to use the manually installed Boost
-#   CHECK: using existing cgal.package
-#- Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
-#  pull in MPI)
-#   CHECK: using existing vtk.package
-#- Build VTK (so that the Ubuntu version doesn't pull in MPI)
-#- Build HDF5 with parallel suppport  (so that the Ubuntu version
-#  doesn't pull in MPI)
-#- Build SCOTCH and PaStiX with support for 64 bit integers
-#- Build PETSc, SLEPc and Trilinos, linking to the above libraries.
+#(x) Most important is ATLAS for BLAS (if MKL is not available)
+#    CHECK: added atlas.package
+#(x) Build LAPACK to use ATLAS BLAS
+#    CHECK: handled as part of ATLAS build
+#(x) Build latest OpenMPI with support for threads turned on. MPICH2
+#    works fine too
+#    CHECK: using existing openmpi.package
+#(x) Build Boost so that Boost.MPI uses the manually installed MPI
+#    CHECK: using existing boost.package, did it detect MPI???
+#(x) Install CGAL to use the manually installed Boost
+#    CHECK: using existing cgal.package
+#(x) Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
+#    pull in MPI)
+#    CHECK: using existing parmetis.package
+#(x) Build VTK (so that the Ubuntu version doesn't pull in MPI)
+#    CHECK: using existing vtk.package
+#(!) Build HDF5 with parallel suppport  (so that the Ubuntu version
+#    doesn't pull in MPI)
+#(x) CHECK: added hdf5.package
+#(!) Build SCOTCH with support for 64 bit integers
+#(!) Build PaStiX with support for 64 bit integers
+#(!) Build PETSc, SLEPc and Trilinos, linking to the above libraries.

 # Platform specific variables
 default PETSC_ARCH=linux-gnu-cxx-opt

=== modified file 'dorsal.sh'
--- dorsal.sh   2012-10-21 15:17:00 +0000
+++ dorsal.sh   2012-10-21 15:44:12 +0000
@@ -548,7 +548,7 @@

     # Store timing
     TOC="$(($(date +%s%N)-TIC))"
-    TIMINGS="$TIMINGS"$"\n""$PACKAGE: "$"\t\t""$((TOC/1000000000)) s"
+    TIMINGS="$TIMINGS"$"\n""$PACKAGE: ""$((TOC/1000000000)) s"

 done

=== added file 'FEniCS/packages/hdf5.package'
--- FEniCS/packages/hdf5.package	1970-01-01 00:00:00 +0000
+++ FEniCS/packages/hdf5.package	2012-10-21 15:44:12 +0000
@@ -0,0 +1,22 @@
+NAME=hdf5-1.8.9
+SOURCE=http://www.hdfgroup.org/ftp/HDF5/current/src/
+PACKING=.tar.bz2
+BUILDCHAIN=custom
+
+package_specific_build () {
+
+    # Download and apply patch
+    if [ ! -e cmake_patch.txt ]
+    then
+        wget http://www.hdfgroup.org/ftp/HDF5/current/src/cmake_patch.txt
+        patch -N -Z -p0 < cmake_patch.txt
+    fi
+
+    # Configure and build
+    mkdir -p dorsal_build_dir
+    cd dorsal_build_dir
+    cmake ${CONFOPTS} -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} ..
+    make ${MAKEOPTS} -j ${PROCS}
+    make install
+
+}

=== modified file 'FEniCS/packages/mpfr.package'
--- FEniCS/packages/mpfr.package	2012-05-29 08:10:52 +0000
+++ FEniCS/packages/mpfr.package	2012-10-21 15:44:12 +0000
@@ -8,7 +8,7 @@
     if [ ! -e patches ]
     then
 	wget http://www.mpfr.org/mpfr-2.2.0/patches
-    fi    
+    fi
     patch -N -Z -p1 < patches
     ./configure --prefix=${INSTALL_PATH} --enable-shared=yes
     make -j ${PROCS}

=== modified file 'FEniCS/platforms/contributed/precise-hpc.platform'
--- FEniCS/platforms/contributed/precise-hpc.platform	2012-10-21 15:19:41 +0000
+++ FEniCS/platforms/contributed/precise-hpc.platform	2012-10-21 15:44:12 +0000
@@ -69,25 +69,28 @@
 echo
 read -p "Press any key to continue"
 
-#- Most important is ATLAS for BLAS (if MKL is not available)
-#   CHECK: added atlas.package
-#- Build LAPACK to use ATLAS BLAS
-#   CHECK: handled as part of ATLAS build
-#- Build latest OpenMPI with support for threads turned on. MPICH2
-#  works fine too
-#   CHECK: using existing openmpi.package
-#- Build Boost so that Boost.MPI uses the manually installed MPI
-#   CHECK: using existing boost.package, did it detect MPI???
-#- Install CGAL to use the manually installed Boost
-#   CHECK: using existing cgal.package
-#- Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
-#  pull in MPI)
-#   CHECK: using existing vtk.package
-#- Build VTK (so that the Ubuntu version doesn't pull in MPI)
-#- Build HDF5 with parallel suppport  (so that the Ubuntu version
-#  doesn't pull in MPI)
-#- Build SCOTCH and PaStiX with support for 64 bit integers
-#- Build PETSc, SLEPc and Trilinos, linking to the above libraries.
+#(x) Most important is ATLAS for BLAS (if MKL is not available)
+#    CHECK: added atlas.package
+#(x) Build LAPACK to use ATLAS BLAS
+#    CHECK: handled as part of ATLAS build
+#(x) Build latest OpenMPI with support for threads turned on. MPICH2
+#    works fine too
+#    CHECK: using existing openmpi.package
+#(x) Build Boost so that Boost.MPI uses the manually installed MPI
+#    CHECK: using existing boost.package, did it detect MPI???
+#(x) Install CGAL to use the manually installed Boost
+#    CHECK: using existing cgal.package
+#(x) Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
+#    pull in MPI)
+#    CHECK: using existing parmetis.package
+#(x) Build VTK (so that the Ubuntu version doesn't pull in MPI)
+#    CHECK: using existing vtk.package
+#(!) Build HDF5 with parallel suppport  (so that the Ubuntu version
+#    doesn't pull in MPI)
+#(x) CHECK: added hdf5.package
+#(!) Build SCOTCH with support for 64 bit integers
+#(!) Build PaStiX with support for 64 bit integers
+#(!) Build PETSc, SLEPc and Trilinos, linking to the above libraries.
 
 # Platform specific variables
 default PETSC_ARCH=linux-gnu-cxx-opt

=== modified file 'dorsal.sh'
--- dorsal.sh	2012-10-21 15:17:00 +0000
+++ dorsal.sh	2012-10-21 15:44:12 +0000
@@ -548,7 +548,7 @@
 
     # Store timing
     TOC="$(($(date +%s%N)-TIC))"
-    TIMINGS="$TIMINGS"$"\n""$PACKAGE: "$"\t\t""$((TOC/1000000000)) s"
+    TIMINGS="$TIMINGS"$"\n""$PACKAGE: ""$((TOC/1000000000)) s"
 
 done

Follow ups

Re: Fwd: [Branch ~dorsal-core/dorsal/main] Rev 749: Add package for HDF5
From: Anders Logg, 2012-10-22