[gmx-users] Error in GROMACS installation
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 30 14:09:10 CEST 2011
Monisha Hajra wrote:
> Hi Justin,
>
> I checked carefully. The make command also gave the same error as pasted
> below. How should I deal this error?
>
For Windows systems, Gromacs needs to use internal XDR definitions (rather than
those that are available system-wide on most Unix/Linux machines). It appears
are not being properly defined. I have no experience with Windows machines, but
if you post the following information, perhaps someone can give you some pointers:
1. Your configuration command (and perhaps even the screen output would be
useful here, too)
2. Your config.h file (in the src subdirectory after configuration finishes)
-Justin
> at' follow
> .libs/libxdrf.o:libxdrf.c:(.text+0x31e3): undefined reference to `_xdr_int'
> .libs/libxdrf.o:libxdrf.c:(.text+0x340b): undefined reference to `_xdr_int'
> .libs/libxdrf.o:libxdrf.c:(.text+0x35a6): undefined reference to `_xdr_int'
> .libs/libxdrf.o:libxdrf.c:(.text+0x3785): undefined reference to `_xdr_int'
> .libs/libxdrf.o:libxdrf.c:(.text+0x3a01): undefined reference to `_xdr_int'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xeb): undefined reference to
> `_xdr_float
> '
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x126): undefined reference to
> `_xdr_doub
> le'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x161): undefined reference to
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x1ec): undefined reference to
> `_xdr_u_ch
> ar'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x22f): undefined reference to
> `_xdr_u_ch
> ar'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x265): undefined reference to
> `_xdr_u_ch
> ar'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x293): undefined reference to
> `_xdr_u_ch
> ar'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x2bf): undefined reference to
> `_xdr_u_ch
> ar'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x309): undefined reference to
> `_xdr_u_sh
> ort'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3c4): undefined reference to
> `_xdr_doub
> le'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3ed): undefined reference to
> `_xdr_vect
> or'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x518): undefined reference to
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x56c): undefined reference to
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5e1): undefined reference to
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x60e): undefined reference to
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x63b): undefined reference to
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x668): more undefined references
> to `_xd
> r_int' follow
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x764): undefined reference to
> `_xdr_doub
> le'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7bd): undefined reference to
> `_xdr_floa
> t'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7d4): undefined reference to
> `_xdr_vect
> or'
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x823): undefined reference to
> `_xdr_stri
> ng'
> Creating library file: .libs/libgmx.dll.a
> collect2: ld returned 1 exit status
> make[4]: *** [libgmx.la <http://libgmx.la>] Error 1
> make[4]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc/gmxlib'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc'
> make: *** [all-recursive] Error 1
>
> On Wed, Mar 30, 2011 at 1:54 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Monisha Hajra wrote:
>
> Hi All,
>
> I am installing GROMACS using cygwin.
>
> I am following the steps as mentioned :
> http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO
>
> *no 5, make install command give the following error in the end :*
>
>
> What was your configuration command? Did "make" work properly?
> It's odd that "make install" fails if "make" works. Do you have
> proper permissions to install in this directory? Configuration and
> compilation are done locally, but installation (if left at default
> settings) is system-wide.
>
> The actual error message is above what you have posted here.
>
> ng'
> Creating library file: .libs/libgmx.dll.a
> collect2: ld returned 1 exit status
> make[3]: *** [libgmx.la <http://libgmx.la> <http://libgmx.la>]
> Error 1
>
> make[3]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc/gmxlib'
> make[2]: *** [install-recursive] Error 1
> make[2]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc/gmxlib'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory
> `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s
> rc'
> make: *** [install-recursive] Error 1
>
> and* make links command gives the following error:*
> *
>
>
> Certainly "make links" will fail if the actual installation failed.
>
> -Justin
>
> *
>
> *
> $ make links
> cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
> for i in $programs; do \
> (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ;
> exit 0); \
> done
> /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or
> directory
> make: *** [links] Error 1
>
> Can anyone de-code thsi error and help me how should I
> successfully proceed for the same.
> Thanks in advance.
>
> Monisha *
>
>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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