Hi Ross
Thanks very much for the advice. I've adopted your suggested .bashrc format and
abandoned setting the MKL_HOME environment. However, when I now implement the
"make serial" command, I get the following error message:
Starting installation of Amber8 (serial) at Thu Oct 14 18:18:18 BST 2004.
mkdir ../exe
mkdir: cannot create directory `../exe': File exists
make: [serial] Error 1 (ignored)
cd lib; make install
make[1]: Entering directory `/root/Hayden/AMBER8/amber8/src/lib'
cpp -traditional -P -I/root/Hayden/AMBER8/amber8/src/include new2oldparm.f >
_new2oldparm.f
ifort -c -w95 -tpp7 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
ifort: error: could not find directory in which g++ resides
make[1]: *** [new2oldparm.o] Error 1
make[1]: Leaving directory `/root/Hayden/AMBER8/amber8/src/lib'
make: *** [serial] Error 2
I tried putting in the -i flag to ignore the error messages and that resulted in
the compilation completing. However, when I typed,
cd $AMBERHOME/test
make test
I got the following message:
cd dmp; ./Run.dmp
.../../exe/sander: Command not found.
./Run.dmp: Program error
make: *** [test.sander.no_lmod] Error 1
so presumably sander isn;t compiling correctly.
Any more advice?
regards
Hayden
> Hi Hayden,
>
> > export AMBERHOME=/root/Hayden/AMBER8/amber8
> > export LD_LIBRARY_PATH=/opt/intel_fc_80/lib
> > export PATH=$AMBERHOME/exe:$PATH
> > export LD_LIBRARY_PATH=$LD_LIBARY_PATH:/opt/intel_fc_80/lib/
>
> Why the two entries for LD_LIBRARY_PATH here? You are better off deleting
> the LD_LIBRARY_PATH variables and setting the following:
>
> export AMBERHOME=/root/Hayden/AMBER8/amber8
> export PATH=$AMBERHOME/exe:$PATH
> source /opt/intel_fc_80/bin/ifortvars.sh
>
> This will use intel's own script to set up your compiler environment (much
> better).
>
> Remember to close your shell and open a new one if you change your .bashrc
> file.
>
> > MKL_HOME is set to /opt/intel_fc_80:/opt/intel_fc_80
> > MKL libraries were not found !
>
> > export MKL_HOME=/opt/intel_fc_80
> > export MKL_HOME=$MKL_HOME:/opt/intel_fc_80
>
> > Is it that my MKL library doesn;t exist?
> > Or
> > That the system is looking for the library in the wrong place?
>
> It could be either. But more likely you don't have the mkl libraries
> installed. These do not come with the intel compiler they have to be
> downloaded seperately. A pain I know but this is how intel licences them.
>
> For example my mkl libraries are in:
>
> /opt/intel/mkl61
>
> If you don't want to bother with the MKL libraries (they only make a very
> small speed improvement) then just remove the MKL_HOME statements from your
> .bashrc file. Close the shell, reopen it and then run the ./configure script
> again.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
>
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Received on Thu Oct 14 2004 - 18:53:00 PDT
