NAMD-2.12-intel-2017.01 issue

[shahzebsiddiqui]

I am having trouble building NAMD with both intel and foss toolchain. Does anyone know how to fix this.

[hpcswadm@amrndhl1157 NAMD]$ cat NAMD-2.12-intel-2017.01.eb 
name = 'NAMD'
version = '2.12'
#version = '2.10b1'
#versionsuffix = '-mpi'

homepage = 'http://www.ks.uiuc.edu/Research/namd/'
description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of
 large biomolecular systems."""

toolchain = {'name': 'intel', 'version': '2017.01'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}

sources = ['NAMD_%(version)s_Source.tar.gz']

dependencies = [
    ('Tcl', '8.6.5'),
]

# /bin/csh is required by 'config' script
osdependencies = ['tcsh']

charm_arch = 'mpi-linux-x86_64'

moduleclass = 'chem'

[hpcswadm@amrndhl1157 NAMD]$ eb NAMD-2.12-intel-2017.01.eb --package --robot
== temporary log file in case of crash /dev/shm/tmp/eb-TwjmNH/easybuild-xrQnQO.log
== resolving dependencies ...
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/Tcl/Tcl-8.6.5-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/Tcl/.8.6.5...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /nfs/grid/software/RHEL7/easybuild/software/MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/Tcl/8.6.5/easybuild/easybuild-Tcl-8.6.5-20170329.114556.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/NAMD/NAMD-2.12-intel-2017.01.eb
== building and installing MPI/intel/2017.1.132-GCC-5.4.0-2.27/impi/2017.1.132/NAMD/2.12...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== FAILED: Installation ended unsuccessfully (build directory: /dev/shm/easybuild/build/NAMD/2.12/intel-2017.01): build failed (first 300 chars): cmd " make -j 80 " exited with exitcode 2 and output:
if [ ! -d inc ]; then mkdir -p inc; fi
if [ ! -d obj ]; then mkdir -p obj; fi
mpiicc -Isrc -I/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded/include -DNAMD_TCL -O3 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -DNAMD_VERSION=\"2.12\"
== Results of the build can be found in the log file(s) /dev/shm/tmp/eb-TwjmNH/easybuild-NAMD-2.12-20170329.114557.GznTl.log
ERROR: Build of /hpc/hpcswadm/easybuild/NAMD/NAMD-2.12-intel-2017.01.eb failed (err: 'build failed (first 300 chars): cmd " make -j 80 " exited with exitcode 2 and output:\nif [ ! -d inc ]; then mkdir -p inc; fi\nif [ ! -d obj ]; then mkdir -p obj; fi\nmpiicc -Isrc -I/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded/include -DNAMD_TCL -O3 -xHost -ftz -fp-speculation=safe -fp-model source -

Log File: easybuild-NAMD-2.12-20170329.114557.GznTl.txt

[pneerincx]

Hi Shahzeb, I'm not familiar with this package, but from the log it looks like you are missing a dependency: ` src/SimParameters.C(42): catastrophic error: cannot open source file "sfftw.h"

include

` based on that error I think you may be running into this problem: https://sourceforge.net/p/mixxx/mailman/message/4342281/ http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/4205.html Hope this helps, Pieter

[shahzebsiddiqui]

I tried to rebuild FFTW, with the FFTW easyblock. I see that the link states that the sfftw.h is for floating point. So I expect the header file should be present since the easyblock takes care of this, I don't see the header files after the rebuild

[hpcswadm@amrndhl1157 ~]$ ls -l /nfs/grid/software/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/FFTW/3.3.4/include
total 708
-rw-r--r-- 1 hpcswadm hpcswadm  2447 Mar 29 16:11 fftw3.f
-rw-r--r-- 1 hpcswadm hpcswadm 54273 Mar 29 16:11 fftw3.f03
-rw-r--r-- 1 hpcswadm hpcswadm 17900 Mar 29 16:11 fftw3.h
-rw-r--r-- 1 hpcswadm hpcswadm 26820 Mar 29 16:11 fftw3l.f03
-rw-r--r-- 1 hpcswadm hpcswadm 18678 Mar 29 14:18 fftw3l-mpi.f03
-rw-r--r-- 1 hpcswadm hpcswadm 36969 Mar 29 14:18 fftw3-mpi.f03
-rw-r--r-- 1 hpcswadm hpcswadm  9624 Mar 29 14:18 fftw3-mpi.h
-rw-r--r-- 1 hpcswadm hpcswadm 25413 Mar 29 16:11 fftw3q.f03