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

From: Nicolas SAPAY <nicolas.sapay.cermav.cnrs.fr>
Date: Fri, 31 Jul 2009 13:55:18 +0100

Thanks for your comments,

> 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

This make sense. Unfortunately, many people prefer/have to use the good
old GNU compiler. Actually, I was suspecting something related to gcc3/4,
but I wanted more information before messing up with the configuration
files...

> 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.cermav.cnrs.fr>
> To: <amber.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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
[ 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 19:56:44 PDT
Custom Search