HPC/Applications/meep

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