[gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: Hi Justin, I thought I might stop clogging the other people's inboxes, and mail you directly. It's better to keep things on the list. I don't necessarily have a final solution; maybe someone else will! I tried installing only the double precision version, and it failed the same way, so I tried doing the single precision, make distclean, and then the double precision. Exactly the same error: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library The contents of the lib directory now: -sh-3.2$ cd fftw/lib/ -sh-3.2$ ls -l total 4464 -rw-r--r-- 1 grahamk uowstf 2230376 Jun 30 15:28 libfftw3.a -rw-r--r-- 1 grahamk uowstf 2200524 Jun 30 15:24 libfftw3f.a -rwxr-xr-x 1 grahamk uowstf 956 Jun 30 15:24 libfftw3f.la -rw-r--r-- 1 grahamk uowstf 44862 Jun 30 15:24 libfftw3f_threads.a -rwxr-xr-x 1 grahamk uowstf 980 Jun 30 15:24 libfftw3f_threads.la -rwxr-xr-x 1 grahamk uowstf 953 Jun 30 15:28 libfftw3.la -rw-r--r-- 1 grahamk uowstf 44722 Jun 30 15:28 libfftw3_threads.a -rwxr-xr-x 1 grahamk uowstf 977 Jun 30 15:28 libfftw3_threads.la drwxr-xr-x 2 grahamk uowstf4096 Jun 30 15:28 pkgconfig -sh-3.2$ Indeed, now I am stuck. Your /lib directory contains what it should, as far as I can tell. Any warnings/errors from the compiler that would suggest something broke? There may also be some other useful diagnostic information in config.log. -Justin Thanks again, and sorry to be a pain. Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Installation with non standard location of fftw3
Hi, I have to install gromacs on a 30 node cluster computer. I only have access to a specific space on the cluster, and it didn't have fftw3 installed on it. I have installed it, and set the CPPFLAGS and LDFLAGS environment variables as per instructions. The include and lib directories exist, and the environment variables are correct. When I tried to install without fftw3 installed I got the following: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) Now with the environment variables set I get: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library fftw3 is installed in /hpc/software/packages/chemistry/fftw The export commands are: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib as per installation documentation: * GROMACS tries to find FFTW and all optional libraries (like Lesstif and FFTW) automatically, but this requires that they are present in the default places where the system searches for include files and libraries. If this is not the case (for instance, your system might not look in /usr/local/include and /usr/local/lib where FFTW is placed) you can tell configure to include these catalogues by using the variables CPPFLAGS and LDFLAGS for includes and libraries, respectively. For instance, assume we have installed FFTW with --prefix=/home/joe/fftw. ... or, if you are using a bash shell: * export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib Both of these directories exist, and the fftw install seemed to run without errors. Any help would be greatly appreciated, as I am running out of ideas. I have tried to find the faq page, but without success. Thanks. Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: Hi, I have to install gromacs on a 30 node cluster computer. I only have access to a specific space on the cluster, and it didn't have fftw3 installed on it. I have installed it, and set the CPPFLAGS and LDFLAGS environment variables as per instructions. The include and lib directories exist, and the environment variables are correct. When I tried to install without fftw3 installed I got the following: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) Now with the environment variables set I get: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library fftw3 is installed in /hpc/software/packages/chemistry/fftw The export commands are: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. -Justin as per installation documentation: * GROMACS tries to find FFTW and all optional libraries (like Lesstif and FFTW) automatically, but this requires that they are present in the default places where the system searches for include files and libraries. If this is not the case (for instance, your system might not look in /usr/local/include and /usr/local/lib where FFTW is placed) you can tell configure to include these catalogues by using the variables CPPFLAGS and LDFLAGS for includes and libraries, respectively. For instance, assume we have installed FFTW with --prefix=/home/joe/fftw. ... or, if you are using a bash shell: * export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib Both of these directories exist, and the fftw install seemed to run without errors. Any help would be greatly appreciated, as I am running out of ideas. I have tried to find the faq page, but without success. Thanks. Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Installation with non standard location of fftw3
Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? How did you install FFTW? What are the contents of the /lib directory? -Justin Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Installation with non standard location of fftw3
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:57 PM To: Gromacs Users' List Subject: Re: [gmx-users] Installation with non standard location of fftw3 Graham Kettlewell wrote: Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? How did you install FFTW? What are the contents of the /lib directory? I installed fftw3.2.1 using the tarball. As I remember it was: tar -xzvf fftw-3.2.1.tar.gz mkdir ../fftw cd fftw-3.2.1 ./configure --prefix /hpc/software/packages/chemistry/fftw make make install I retyped this, so... The contents of lib are: -sh-3.2$ cd lib/ -sh-3.2$ ls -l total 2196 -rw-r--r-- 1 grahamk uowstf 2230376 Jun 30 10:02 libfftw3.a -rwxr-xr-x 1 grahamk uowstf 951 Jun 30 10:02 libfftw3.la drwxr-xr-x 2 grahamk uowstf4096 Jun 30 10:02 pkgconfig Cheers, graham -Justin Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:57 PM To: Gromacs Users' List Subject: Re: [gmx-users] Installation with non standard location of fftw3 Graham Kettlewell wrote: Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? How did you install FFTW? What are the contents of the /lib directory? I installed fftw3.2.1 using the tarball. As I remember it was: tar -xzvf fftw-3.2.1.tar.gz mkdir ../fftw cd fftw-3.2.1 ./configure --prefix /hpc/software/packages/chemistry/fftw make make install I retyped this, so... The contents of lib are: -sh-3.2$ cd lib/ -sh-3.2$ ls -l total 2196 -rw-r--r-- 1 grahamk uowstf 2230376 Jun 30 10:02 libfftw3.a -rwxr-xr-x 1 grahamk uowstf 951 Jun 30 10:02 libfftw3.la drwxr-xr-x 2 grahamk uowstf4096 Jun 30 10:02 pkgconfig OK, that explains it. You don't have the libfftwf.a and libfftwf.la that the configure script is looking for. The recommended installation procedure (creating single- and double-precision versions) is: ./configure --enable-threads --enable-float make make install make distclean ./configure --enable-threads make make install -Justin Cheers, graham -Justin Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
