AMBER Archive (2009)

Subject: Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Jul 31 2009 - 07:33:52 CDT

gfortran is not supported as a compiler for pmemd. For a linux system you
need to be using either ifort, pathf90, pgf90 - one of these commercial
compilers that actually have good performance. I don't know what the
current story is for gfortran in terms of performance and compliance to
standards. Some folks HAVE dinked with getting the free compilers to
compile pmemd, but it requires dinking around, so they will have to comment
on the problems further (ie., somebody else on the list may have their own
hacked-up config.h for pmemd and gfortran, but I don't). The problem that
you are having here looks to me most likely to be that the compiler is not
recognizing a trailing line continuation marker properly - just a guess, and
looking at the source, I can't really tell (looks like it may be lost in the
comment lines, or some such).
Regards - Bob Duke
----- Original Message -----
From: "Nicolas SAPAY" <nicolas.sapay_at_cermav.cnrs.fr>
To: <amber_at_ambermd.org>
Sent: Friday, July 31, 2009 5:41 AM
Subject: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits

Hello everybody,

I've got some hard time compiling pmemd on a fedora9 64 bits. I use the
following command line to configure the installation:

./configure linux_em64t f90 lam fftw bintraj
amber is in : home/software/amber10
lam is in : /usr/lib64/lam
fftw is in : /home/software/fftw-3.2.1
netCDF is in : /home/software/netcdf-4.0.1

The AMBERHOME and MPI_HOME variables have been set accordingly. The
configuration runs smoothly, but the compilation fails with the following
errors:

$ make install
cd src && make install
make[1]: enter in directory « /home/software/amber10/src/pmemd/src »
/lib/cpp -P -I/home/software/fftw-3.2.1/incude -I/usr/lib64/lam/include
-DFFTW_FFT -DBINTRAJ -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS
-DDIRFRC_NOVEC gbl_constants.fpp gbl_constants.f90
gfortran -old_rl -c -O3 -msse3 gbl_constants.f90
/lib/cpp -P -I/home/software/fftw-3.2.1/incude -I/usr/lib64/lam/include
-DFFTW_FFT -DBINTRAJ -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS
-DDIRFRC_NOVEC gbl_datatypes.fpp gbl_datatypes.f90
gbl_datatypes.fpp:18:18: error: missing terminating ' character
gbl_datatypes.fpp:30:54: error: missing terminating ' character
gbl_datatypes.fpp:39:55: error: missing terminating ' character
gbl_datatypes.fpp:49:55: error: missing terminating ' character
gbl_datatypes.fpp:56:58: error: missing terminating ' character
gbl_datatypes.fpp:63:57: error: missing terminating ' character
...
make[1]: *** [fft1d.o] Error 1
make[1]: leaving directory « /home/software/amber10/src/pmemd/src » make:
*** [install] Error 2

Does someone have a suggestion to fix this problem? Note that gcc4.3 is
installed on my system.

Thanks a lot,
Nicolas 

-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
Phone: +33 (0)4 76 03 76 44/53

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