[gmx-users] Installation error

[Mark Abraham]

On 15/04/2011 12:29 AM, pawan raghav wrote:
> I have already posted this error report on 6 Dec 2010 but still have 
> not getting any solution. So I am thankful if any one can rectify the 
> solution of installation problem i.e. While installing gromacs-4.5.3 I 
> got an error on executing make command. I am installing this gromacs 
> version on cygwin. The error written below, please tell me solution of 
> this error.

Apparently you have some kind of XDR library linking issue. Perhaps that 
is caused by some other library floating around. GROMACS has its own 
version if the system one is broken, but perhaps some Windows DLL is 
confusing things.

My Cygwin install builds with cmake perfectly. I haven't tried configure 
in a long while.

Mark

> Creating library file: .libs/libgmx.dll.a
>
> .libs/checkpoint.o:checkpoint.c:(.text+0xcd): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x13c): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x236): undefined reference to 
> `_xdr_double'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x256): undefined reference to 
> `_xdr_vector'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3f0): undefined reference to 
> `_xdr_float'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x408): undefined reference to 
> `_xdr_vector'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x64e): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0xfad): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0xff0): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x10a3): undefined reference to 
> `_xdr_double'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x10bb): undefined reference to 
> `_xdr_vector'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x127d): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x12c0): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x1372): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x138a): undefined reference to 
> `_xdr_vector'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x1fb9): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x24cf): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x256a): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2606): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2642): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x26d4): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2755): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2791): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x27de): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x283a): undefined reference to 
> `_xdr_u_char'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x287a): undefined reference to 
> `_xdr_u_char'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x28ba): undefined reference to 
> `_xdr_u_char'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x28fa): undefined reference to 
> `_xdr_u_char'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x293a): undefined reference to 
> `_xdr_u_char'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x297a): more undefined 
> references to `_xdr_u_char' follow
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2f00): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2f8e): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x2ffc): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3070): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x30e4): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3158): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x31cc): more undefined 
> references to `_xdr_string' follow
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3236): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x328f): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x32d3): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x334a): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3412): undefined reference to 
> `_xdr_double'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3457): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x34b1): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3501): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3551): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x358e): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x35d2): more undefined 
> references to `_xdr_int' follow
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x392f): undefined reference to 
> `_xdr_string'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3a31): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x3a75): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x4cb4): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x5216): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x6c90): undefined reference to 
> `_xdr_int'
>
> .libs/checkpoint.o:checkpoint.c:(.text+0x76ca): more undefined 
> references to `_xdr_int' follow
>
> .libs/enxio.o:enxio.c:(.text+0xc72): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xc91): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xcc3): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xcf9): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xd18): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xd40): more undefined references to 
> `_xdr_string' follow
>
> .libs/enxio.o:enxio.c:(.text+0xdba): undefined reference to `_xdr_int'
>
> .libs/enxio.o:enxio.c:(.text+0xdd7): undefined reference to `_xdr_int'
>
> .libs/enxio.o:enxio.c:(.text+0xe62): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xe81): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xeb3): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xf43): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xf62): undefined reference to `_xdr_string'
>
> .libs/enxio.o:enxio.c:(.text+0xfe4): more undefined references to 
> `_xdr_string' follow
>
> .libs/gmxfio.o:gmxfio.c:(.text+0x728): undefined reference to 
> `_xdrstdio_create'
>
> .libs/gmxfio.o:gmxfio.c:(.text+0xd39): undefined reference to 
> `_xdrstdio_create'
>
> .libs/xdrd.o:xdrd.c:(.text+0x30): undefined reference to `_xdr_int'
>
> .libs/xdrd.o:xdrd.c:(.text+0x40): undefined reference to `_xdr_int'
>
> .libs/xdrd.o:xdrd.c:(.text+0x81): undefined reference to `_xdr_float'
>
> .libs/xtcio.o:xtcio.c:(.text+0xb7): undefined reference to `_xdr_int'
>
> .libs/xtcio.o:xtcio.c:(.text+0xd8): undefined reference to `_xdr_int'
>
> .libs/xtcio.o:xtcio.c:(.text+0x13c): undefined reference to `_xdr_int'
>
> .libs/xtcio.o:xtcio.c:(.text+0x18c): undefined reference to `_xdr_float'
>
> .libs/xtcio.o:xtcio.c:(.text+0x23c): undefined reference to `_xdr_float'
>
> .libs/xtcio.o:xtcio.c:(.text+0x257): undefined reference to `_xdr_float'
>
> .libs/xtcio.o:xtcio.c:(.text+0x272): undefined reference to `_xdr_float'
>
> .libs/xtcio.o:xtcio.c:(.text+0x28d): undefined reference to `_xdr_float'
>
> .libs/xtcio.o:xtcio.c:(.text+0x2a8): more undefined references to 
> `_xdr_float' follow
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x51f): undefined reference to `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x537): undefined reference to `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x54f): undefined reference to `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x575): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x58d): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x5a5): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x5bd): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x5d5): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x5ed): more undefined references to 
> `_xdr_float' follow
>
> .libs/libxdrf.o:libxdrf.c:(.text+0xacd): undefined reference to `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0xbfc): undefined reference to `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x2159): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x2190): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x247c): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x24b2): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x2505): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x25b3): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x262e): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x2642): undefined reference to 
> `_xdr_vector'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x26a0): undefined reference to 
> `_xdr_float'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x26b8): undefined reference to 
> `_xdr_vector'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x2786): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x27a8): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x27c7): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x27e2): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x27fd): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x2a24): more undefined references to 
> `_xdr_int' follow
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x3803): undefined reference to 
> `_xdr_opaque'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x3852): undefined reference to 
> `_xdr_opaque'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x40bd): undefined reference to 
> `_xdr_int'
>
> .libs/libxdrf.o:libxdrf.c:(.text+0x437a): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x13d): undefined reference to 
> `_xdr_float'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x194): undefined reference to 
> `_xdr_double'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x1ce): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x267): undefined reference to 
> `_xdr_double'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x286): undefined reference to 
> `_xdr_vector'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x2d7): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x325): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x342): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x35f): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x37c): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x399): more undefined 
> references to `_xdr_u_char' follow
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x4ef): undefined reference to 
> `_xdr_u_short'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x532): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x57a): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5ae): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5e0): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x84d): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x88c): undefined reference to 
> `_xdr_string'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x90b): undefined reference to 
> `_xdr_float'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x92a): undefined reference to 
> `_xdr_vector'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x970): undefined reference to 
> `_xdr_double'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x9a6): undefined reference to 
> `_xdr_double'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x9c2): undefined reference to 
> `_xdr_float'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xa98): undefined reference to 
> `_xdr_u_short'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xab7): undefined reference to 
> `_xdr_u_char'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xad6): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xaed): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xb04): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xb23): undefined reference to 
> `_xdr_int'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xd30): undefined reference to 
> `_xdr_float'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xd53): undefined reference to 
> `_xdr_vector'
>
> .libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xd64): undefined reference to 
> `_xdr_double'
>
> collect2: ld returned 1 exit status
>
> make[4]: *** [libgmx.la <http://libgmx.la/>] Error 1
>
> make[4]: Leaving directory `/cygdrive/c/gromacs-4.5.3/src/gmxlib'
>
> make[3]: *** [all-recursive] Error 1
>
> make[3]: Leaving directory `/cygdrive/c/gromacs-4.5.3/src/gmxlib'
>
> make[2]: *** [all-recursive] Error 1
>
> make[2]: Leaving directory `/cygdrive/c/gromacs-4.5.3/src'
>
> make[1]: *** [all] Error 2
>
> make[1]: Leaving directory `/cygdrive/c/gromacs-4.5.3/src'
>
> make: *** [all-recursive] Error 1
>
>
>
> -- 
> Pawan

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