HPC/Applications/meep
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Distribution
- http://ab-initio.mit.edu/wiki/index.php/Meep
- http://ab-initio.mit.edu/wiki/index.php/Meep_Installation
Supporting Packages
blas, lapack
- needed for harminv (not speed-critical)
- CentOS blas and lapack collide with RHEL libgfortran:
Transaction Check Error: package libgfortran-4.1.2-14.el5 (which is newer than libgfortran-4.1.1-52.el5.2) is already installed
- This is RedHat's 64-bit version: libgfortran-4.1.2-14.el5.x86_64 – 32bit version is missing!
We have:
[root@mgmt01 redhat]# locate '*libgfortran*rpm' /drbd/exports/opt/centos/5.0/os/x86_64/CentOS/libgfortran-4.1.1-52.el5.i386.rpm /drbd/exports/opt/centos/5.0/os/x86_64/CentOS/libgfortran-4.1.1-52.el5.x86_64.rpm /drbd/exports/opt/centos/5.0/updates/x86_64/RPMS/libgfortran-4.1.1-52.el5.2.i386.rpm /drbd/exports/opt/centos/5.0/updates/x86_64/RPMS/libgfortran-4.1.1-52.el5.2.x86_64.rpm /drbd/exports/opt/centos/5.0/updates-staged/x86_64/RPMS/libgfortran-4.1.1-52.el5.2.i386.rpm /drbd/exports/opt/centos/5.0/updates-staged/x86_64/RPMS/libgfortran-4.1.1-52.el5.2.x86_64.rpm /drbd/exports/opt/centos/5.1/os/x86_64/CentOS/libgfortran-4.1.2-14.el5.i386.rpm /drbd/exports/opt/centos/5.1/os/x86_64/CentOS/libgfortran-4.1.2-14.el5.x86_64.rpm /drbd/exports/opt/rhel/5Server/os/x86_64/Server/libgfortran-4.1.1-52.el5.i386.rpm /drbd/exports/opt/rhel/5Server/os/x86_64/Server/libgfortran-4.1.1-52.el5.x86_64.rpm /drbd/exports/opt/rhel/5Server/updates/x86_64/RPMS/libgfortran-4.1.1-52.el5.2.i386.rpm /drbd/exports/opt/rhel/5Server/updates/x86_64/RPMS/libgfortran-4.1.1-52.el5.2.x86_64.rpm /drbd/exports/opt/rhel/5Server/updates/x86_64/RPMS/libgfortran-4.1.2-14.el5.x86_64.rpm /drbd/exports/opt/rhel/5Server/updates-staged/x86_64/RPMS/libgfortran-4.1.2-14.el5.x86_64.rpm
- Brute force:
rpm -ivh /opt/centos/5.1/os/x86_64/CentOS/libgfortran-4.1.2-14.el5.i386.rpm yum install lapack lapack-devel blas blas-devel
zlib
yum install zlib-devel
FFTW2, FFTW3
- http://www.fftw.org/
- download to
/opt/soft/src/fftw - build in
/opt/soft/build/fftw-*
./BUILD.SH grep -i warn config*.log
TODO: install and configure "environment-modules"
guile
- from RHEL5
yum install guile guile-devel Installing: guile x86_64 5:1.8.0-8.20060831cvs Server 1.4 M guile i386 5:1.8.0-8.20060831cvs Server 1.4 M guile-devel x86_64 5:1.8.0-8.20060831cvs Server 120 k guile-devel i386 5:1.8.0-8.20060831cvs Server 120 k Installing for dependencies: gmp i386 4.1.4-10.el5 Server 665 k gmp-devel x86_64 4.1.4-10.el5 Server 568 k libtool-ltdl i386 1.5.22-6.1 Server 37 k libtool-ltdl x86_64 1.5.22-6.1 Server 37 k
libctl
- http://ab-initio.mit.edu/wiki/index.php/Libctl
- http://ab-initio.mit.edu/libctl/libctl-3.0.3.tar.gz
- download to
/opt/soft/src/meep - build in
/opt/soft/build/libctl-*
./BUILD.SH
HarmInv
- http://ab-initio.mit.edu/wiki/index.php/Harminv_installation
- fails to link with Intel MKL?
- detection failure for sgemm
- not critical; use reference BLAS/LAPACK
- use icpc instead of icc to handle INFINITY or 1.0/0.0 -- Darn:
checking for C complex keyword... _Complex checking for C complex I constant... unsupported configure: error: C doesn't support complex numbers.
- Solution:
CFLAGS=-std=c99
- final:
./BUILD.SH
HDF5
- http://www.hdfgroup.org/
- http://www.hdfgroup.org/HDF5/index.html
- ftp://ftp.hdfgroup.org/HDF5/current/src/
- ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/release_docs/INSTALL – long and detailed instructions
- download to
/opt/soft/src/meep - build in
/opt/soft/build - compiled serial version initially
./BUILD-SERIAL.SH
- TODO:
- http://www.hdfgroup.org/HDF5/PHDF5/ – parallel version
MEEP
- download to
/opt/soft/src/meep - build in
/opt/soft/build/meep-*
./BUILD.SH
- added to
/opt/teamhpc/node-skel/etc/profile.d/cnm.*sh
- build 3 is a chimera, with -llapack, and MKL dependencies, build 4 uses no MKL
- TODO: eval, benchmark