Thanks for the quick reply!
Here are some more details:
1. I untarred Amber 11 and AmberTools 1.4 in /home/linusj/amber, and set $AMBERHOME to /home/linusj/amber/amber11
2. I applied the bug fixes for both Amber 11 and AmberTools 1.4
3. The directory /home/linusj/amber/amber11/AmberTools/src/netcdf/ was created, but it does not contain libnetcdf.a
4. Step-by-step, this was my procedure: 1) untar Amber and AmberTools; 2) apply the patches for Amber (apply_bugfix.x bugfix.all); 3) apply the patch for AmberTools (patch -p0 -N < bugfix.all) -- and no, I didn't use the same "bugfix.all" for both; 4) use "configure intel" in $AMBERHOME/AmberTools/src/ to generate the config.h files; 5) cd $AMBERHOME/src and run "make serial"
5. Our cluster has intel Xeon cpus, and I have the intel compilers loaded as modules -- ifort/10.1.018 and icc/10.1.018
I don't know what else to say... If it helps, here is the full output from when I run "make serial" again:
cd netcdf/src && make install
make[1]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src'
Making install in f90
make[2]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/f90'
make[3]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/f90'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3" || mkdir -p -- "/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3"
/opt/software/gaussian/d02/g03/bsd/install -c -m 644 './netcdf_f90.3' '/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f90.3'
test -z "/home/linusj/amber/amber11/AmberTools/src/netcdf/include" || mkdir -p -- "/home/linusj/amber/amber11/AmberTools/src/netcdf/include"
/opt/software/gaussian/d02/g03/bsd/install -c -m 644 'typesizes.mod' '/home/linusj/amber/amber11/AmberTools/src/netcdf/include/typesizes.mod'
/opt/software/gaussian/d02/g03/bsd/install -c -m 644 'netcdf.mod' '/home/linusj/amber/amber11/AmberTools/src/netcdf/include/netcdf.mod'
make[3]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/f90'
make[2]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/f90'
Making install in fortran
make[2]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/fortran'
make[3]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/fortran'
test -z "/home/linusj/amber/amber11/AmberTools/src/netcdf/lib" || mkdir -p -- "/home/linusj/amber/amber11/AmberTools/src/netcdf/lib"
test -z "/home/linusj/amber/amber11/AmberTools/src/netcdf/include" || mkdir -p -- "/home/linusj/amber/amber11/AmberTools/src/netcdf/include"
/opt/software/gaussian/d02/g03/bsd/install -c -m 644 'netcdf.inc' '/home/linusj/amber/amber11/AmberTools/src/netcdf/include/netcdf.inc'
test -z "/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3" || mkdir -p -- "/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3"
/opt/software/gaussian/d02/g03/bsd/install -c -m 644 './netcdf_f77.3' '/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f77.3'
make[3]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/fortran'
make[2]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/fortran'
Making install in libsrc
make[2]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/libsrc'
make[3]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/libsrc'
test -z "/home/linusj/amber/amber11/AmberTools/src/netcdf/lib" || mkdir -p -- "/home/linusj/amber/amber11/AmberTools/src/netcdf/lib"
/bin/sh ../libtool --mode=install /opt/software/gaussian/d02/g03/bsd/install -c 'libnetcdf.la' '/home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.la'
/opt/software/gaussian/d02/g03/bsd/install -c .libs/libnetcdf.lai /home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.la
/opt/software/gaussian/d02/g03/bsd/install -c .libs/libnetcdf.a /home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
chmod 644 /home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
chmod: cannot access `/home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.a': No such file or directory
make[3]: *** [install-libLTLIBRARIES] Error 1
make[3]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/libsrc'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/libsrc'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src'
make: *** [../netcdf/lib/libnetcdf.a] Error 2
Thanks for the help!
Linus
____________________
Dr Linus Johannissen
Post-doctoral research associate
Manchester Interdisciplinary Biocentre
University of Manchester
UK
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 17 November 2010 16:47
To: AMBER Mailing List
Subject: Re: [AMBER] Amber 11 installation problems
Have you applied the bug fixes?
Also, does the directory /home/linusj/amber/amber11/AmberTools/src/netcdf/
exist? There are far too many variables to really nail down what's
happening here. If you can you send more details about your exact
procedures, your system details (specifically the OS and compiler/compiler
version, etc.), that would help us. Also, the below error message is
unlikely to be the only error message produced by the install process if the
untarring and everything were done properly, since libnetcdf.a should have
been created.
All the best,
Jason
On Wed, Nov 17, 2010 at 11:39 AM, Linus Johannissen <
Linus.Johannissen.manchester.ac.uk> wrote:
> Dear Amber developers and users,
>
> When I try to compile Amber 11 (make serial), I get to the following error
> message:
>
> chmod 644 /home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
> chmod: cannot access
> `/home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.a': No such
> file or directory
> make[3]: *** [install-libLTLIBRARIES] Error 1
> make[3]: Leaving directory
> `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/libsrc'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory
> `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/libsrc'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory
> `/home/linusj/amber/amber11/AmberTools/src/netcdf/src'
> make: *** [../netcdf/lib/libnetcdf.a] Error 2
>
> This is after I untarred both Amber 11 and AmberTools 1.4 into the same
> directory, then run "./configure intel" in the $AMBERHOME/AmberTools/src
> directory to create the config.h file in $AMBERHOME/src. I tried running
> "make clean" before "make serial", but got the same result.
>
> Thanks in advance for any suggestions,
> Linus
>
> ____________________
> Dr Linus Johannissen
> Post-doctoral research associate
> Manchester Interdisciplinary Biocentre
> University of Manchester
> UK
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Nov 17 2010 - 10:00:05 PST
