Re: [gmx-users] How to install GROMACS in 64-bit?
On 29/05/2012 6:37 PM, a a wrote: Dear Sir/Madam, Thanks for the insightful comments from the experts.Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1: ./configure --enable-shared --prefix=/home/softwares/fftw301 make make install In the .bash file: export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib go to the following directory /home/softwares/gromacs-4.5.5: ./configure --enable-shared --prefix=/home/softwares/g455 make = == In the middle of the make, I found this error message: == /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit machine and the OS is also 64 bit, what should I do to make sure both the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings? I would start by observing that those error messages pertain to an installation of FFTW that configure found in /usr/local/lib, and not the one in /home/softwares. You have to sort that out first, since this error messages indicates the need to use FFTW configured with --enable-shared, per the link I gave last time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] How to install GROMACS in 64-bit?
Dear Mark, I have overlook it. Sorry. I have already added the following two sentences in .bashrc file in my home directory (when I login as user). export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib Should I type in another lines? Did I do any common mistakes in using the command export with .bash shell? Should I add these two lines at the root directory as it seems I have a role as root during installation? Please kindly give me some more guidance. Many thanks, Catherine Date: Tue, 29 May 2012 18:48:15 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] How to install GROMACS in 64-bit? On 29/05/2012 6:37 PM, a a wrote: Dear Sir/Madam, Thanks for the insightful comments from the experts. Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1: ./configure --enable-shared --prefix=/home/softwares/fftw301 make make install In the .bash file: export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib go to the following directory /home/softwares/gromacs-4.5.5: ./configure --enable-shared --prefix=/home/softwares/g455 make = == In the middle of the make, I found this error message: == /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit machine and the OS is also 64 bit, what should I do to make sure both the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings? I would start by observing that those error messages pertain to an installation of FFTW that configure found in /usr/local/lib, and not the one in /home/softwares. You have to sort that out first, since this error messages indicates the need to use FFTW configured with --enable-shared, per the link I gave last time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] How to install GROMACS in 64-bit?
On 30/05/2012 1:50 AM, a a wrote: Dear Mark, I have overlook it. Sorry. I have already added the following two sentences in .bashrc file in my home directory (when I login as user). export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib Should I type in another lines? They won't help until you start a new shell. Or, instead, use them on the command line like the installation instructions suggest - since you don't need these settings on an ongoing basis. Did I do any common mistakes in using the command export with .bash shell? Should I add these two lines at the root directory as it seems I have a role as root during installation? Definitely not. make install is the only command for which you should be root, and only then if the installation location requires it. Unless you like pain from risking needing to reinstall your trashed system. Mark Please kindly give me some more guidance. Many thanks, Catherine Date: Tue, 29 May 2012 18:48:15 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] How to install GROMACS in 64-bit? On 29/05/2012 6:37 PM, a a wrote: Dear Sir/Madam, Thanks for the insightful comments from the experts.Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1: ./configure --enable-shared --prefix=/home/softwares/fftw301 make make install In the .bash file: export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib go to the following directory /home/softwares/gromacs-4.5.5: ./configure --enable-shared --prefix=/home/softwares/g455 make = == In the middle of the make, I found this error message: == /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit machine and the OS is also 64 bit, what should I do to make sure both the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings? I would start by observing that those error messages pertain to an installation of FFTW that configure found in /usr/local/lib, and not the one in /home/softwares. You have to sort that out first, since this error messages indicates the need to use FFTW configured with --enable-shared, per the link I gave last time. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
