AMBER Archive (2008)

Subject: Re: AMBER: help to install AMBER9

From: Jeffrey (
Date: Sun May 11 2008 - 04:12:18 CDT

Thanks very much for all suggestions.
The mpich-gm was compiled by the administrator. So now I can't access to a 32-bit lib. However, I will show all your suggestions to our administrator and request for a 32-bit mpich-gm.

I tried to compile a 64-bit amber by removing all "-tp p7" in config.h as Ross's suggestion. But another error report appeared as follows:
.../lib/sys.a: could not read symbols: Memory exhausted
make[1]: *** [sander.MPI] Error 2
make[1]: Leaving directory `/storage/SCSI/st13/home/user/tk/amber9/src/sander'
make: *** [parallel] Error 2

Does it mean that the memory is not enough for generating the AMBER executable?
We have a 8-GB memory in each node.

Thanks in advance.
Have a nice day.

Dear all,

   I am trying to install amber9 on the AMD 64 opteron machines. The parameters used during the configure are:
../configure -bintraj -opteron pgf90

Because the graphical interface can't be accessed, I changed the Makefile as follows:
# If the X-window stuff is not available, or does not work, comment
# out the above line, and uncomment the line below, which will
# compile just the text-only version of LEaP:
       cd leap/src/leap; make -f Makefile.tleap install

But when compiling the leap module, a segmentation error appeared and the compiling halted. Here is the error report:
../utilMakeHelp helptext.text helptext.c
make[1]: *** [helptext.c] Segmentation fault (core dumped)
make[1]: Leaving directory `/storage/SCSI/st13/home/user/tk/amber9/src/leap/src/leap'
make: *** [serial] Error 2

When I commented the line " cd leap/src/leap; make -f Makefile.tleap install " to skip the leap module, everything is ok. The question is, if I don't use LEaP to build the system, whether the other modules will be affected by skipping the LEaP?

For a parallel installation, the following parameters are used:
../configure -bintraj -opteron -mpich pgf90

But the program complained that it couldn't find -lmpichf90 when compiling. I do find the libmpichf90.a in the mpich-gm-1.2.6/lib directory. Here is the error message:

        ../lmod/lmod.a .../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a .../netcdf/lib/libnetcdf.a -L/home/user/tk/opt/mpich-gm-1.2.6/lib -lmpichf90 -lmpich -L/opt/gm/lib/ -lgm
/usr/bin/ld: skipping incompatible /home/user/tk/opt/mpich-gm-1.2.6/lib/libmpichf90.a when searching for -lmpichf90
/usr/bin/ld: cannot find -lmpichf90
make[1]: *** [sander.MPI] Error 2
make[1]: Leaving directory `/storage/SCSI/st13/home/user/tk/amber9/src/sander'
make: *** [parallel] Error 2

  Could someone please give me some suggestions on how to fix this problem?

Thanks for the time.



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