When I directly used gnu compilers it gave the following error. Then as
instructed I used '-nofftw3' flag. This shows the gcc version.
......
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
No patches available
Searching for python2... Found python2.5:
/usr/local/MGLTools-1.5.1/mgltools_i86Linux2_1.5.1/bin/python2.5
Obtaining the gnu suite version:
gcc -v
The version is 4.1.2
ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU
compiler.
Please re-run configure with the '-nofftw3' flag to use this
compiler:
./configure -nofftw3 gnu
.........................................................................................
I commented MKL_HOME environment variable, but still the compilation is not
complete.. Final part of the error msg are as follows.
-- Warning: Obsolete: arithmetic IF statement at (1)
In file pubfft.F90:290
if (nr) 101,105,101
1
Warning: Obsolete: arithmetic IF statement at (1)
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -I/home/srg/nadun/ambertools/amber12/include -o cluster.o
cluster.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -I/home/srg/nadun/ambertools/amber12/include -o clusterLib.o
clusterLib.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 \
-o rdparm main.o rdparm.o dispatch.o help.o utility.o
second.o io.o trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o
mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o
actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o
-L/home/srg/nadun/ambertools/amber12/lib -lpdb -larpack -llapack -lblas
-lgfortran -w -L/home/srg/nadun/ambertools/amber12/lib -lnetcdf -lm
/usr/bin/ld: cannot find -lnetcdf
collect2: ld returned 1 exit status
make[2]: *** [rdparm] Error 1
make[2]: Leaving directory
`/home/srg/nadun/ambertools/amber12/AmberTools/src/ptraj'
make[1]: *** [serial] Error 2
make[1]: Leaving directory
`/home/srg/nadun/ambertools/amber12/AmberTools/src'
Thank you
On Sat, May 4, 2013 at 6:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Could you provide some more information, such as what versions of
> compilers you are trying to use, and what flags you passed to
> configure? Aside from that, a few things may be causing issues:
>
> On Sat, May 4, 2013 at 2:21 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>
> wrote:
> > make[3]: Warning: File `nxtsec.o' has modification time 1.9e+02 s in the
> > future
> > make[3]: `nxtsec.o' is up to date.
> > make[3]: `random.o' is up to date.
> > make[3]: warning: Clock skew detected. Your build may be incomplete.
>
> I don't think this is the key issue but it could be a problem in the
> future. The 'make' program uses file time stamps to decide whether or
> not something needs to be built, so sometimes things might not be
> built in the right order. This can happen if for example you are
> compiling on an NFS mount and its clock and yours are out of sync.
> Make sure your system time is correct.
>
> > gfortran: /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_intel_lp64.a: No such
> > file or directory
>
> It seems like the build has problems with the MKL on your system
> (which is very old at this point). Try building without MKL (unset
> MKL_HOME) or make sure you use the '-oldmkl' flag.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Sat May 04 2013 - 17:30:03 PDT
