[gmx-users] Error in GROMACS installation

[Monisha Hajra]

Hi Justin,

I checked carefully. The make command also gave the same error as pasted
below. How should I deal this error?

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] 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> 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>] 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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