fftw-3.3 installation: first gone to the fftw3.3 folder ./configure --enable-threads --enable-float --enable-sse --enable-shared --prefix /home/ganguly/Gromacs/fftw3.3 . . . make . . . make install
Then gromacs 4.5.5 is being installed. installation: first gone to the gromacs-4.5.5 folder ./configure --disable-shared [also done for ./configure --enable-shared] . . . make . . . make install same error is coming. The error is given below: After make command, the last few lines are this type:::-- make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html' Making all in images make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images' Making all in online make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online' make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html' make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' Making all in man make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' Making all in man1 make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1' Making all in man7 make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7' make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5' Then after the make install command :- [ganguly@localhost gromacs-4.5.5]$ make install Making install in include . . . . . /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/futil.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gbutil.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gen_ad.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/genborn.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ana.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_arpack.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_blas.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_cyclecounter.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fatal.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fft.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ga2la.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_lapack.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_matrix.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_parallel_3dfft.h': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make: *** [install-recursive] Error 1 [ganguly@localhost gromacs-4.5.5]$ ________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j...@um.es] Sent: Wednesday, January 11, 2012 5:12 PM To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) You need to post how did you exactly installed fftw and gromacs in order to get more help. It seems to me that the problem is related to the shared fftw libraries. Could you compile the gromacs binaries with --disable-shared? Javier El 11/01/12 12:07, Anik Sen escribió: I have already done that but the problem persisits. ________________________________ From: gmx-users-boun...@gromacs.org<mailto:gmx-users-boun...@gromacs.org> [gmx-users-boun...@gromacs.org<mailto:gmx-users-boun...@gromacs.org>] on behalf of Javier Cerezo [j...@um.es<mailto:j...@um.es>] Sent: Wednesday, January 11, 2012 1:56 PM To: gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> Subject: Re: [gmx-users] (no subject) Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest. The error file is given below: /usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_d.la<http://libmd_d.la/>] Error 1 make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 Thanx in advance Anik ======================================================== Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] ======================================================== -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434 -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434
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