Hi,
Actually, I have managed to install amber9 in HPC machine (Xeon x86_64, intel mpi/mkl/compilers) with options below:
../configure -intelmpi -opteron -verbose -mmtsb -bintraj ifort_x86_64
whereby the FC and LOAD option in config.h was changed from ifort to mpiifort.
Then, I used the same method above to install amber9 in SMP machine (IA64, LAM MPI,intel mkl,GNU compilers with options below but failed:
../configure -lam -<there_is_no_IA64_platform_option> -verbose -mmtsb -bintraj gfortran
As you can see, there isn't any platform option for IA64 in the configure -help option.
The errors are as below:
netcdf.f90:(.text+0x48072): undefined reference to `nf_get_varm_double_'
netcdf.f90:(.text+0x481d2): undefined reference to `nf_get_vars_double_'
netcdf.f90:(.text+0x482a2): undefined reference to `nf_get_vara_double_'
.../netcdf/lib/libnetcdf.a(netcdf.o): In function `__netcdf__nf90_get_var_5d_eightbytereal':
netcdf.f90:(.text+0x48ad2): undefined reference to `nf_get_varm_double_'
netcdf.f90:(.text+0x48c52): undefined reference to `nf_get_vars_double_'
netcdf.f90:(.text+0x48d42): undefined reference to `nf_get_vara_double_'
.../netcdf/lib/libnetcdf.a(netcdf.o): In function `__netcdf__nf90_get_var_6d_eightbytereal':
netcdf.f90:(.text+0x495f2): undefined reference to `nf_get_varm_double_'
netcdf.f90:(.text+0x49782): undefined reference to `nf_get_vars_double_'
netcdf.f90:(.text+0x49882): undefined reference to `nf_get_vara_double_'
.../netcdf/lib/libnetcdf.a(netcdf.o): In function `__netcdf__nf90_get_var_7d_eightbytereal':
netcdf.f90:(.text+0x4a1d2): undefined reference to `nf_get_varm_double_'
netcdf.f90:(.text+0x4a382): undefined reference to `nf_get_vars_double_'
netcdf.f90:(.text+0x4a4a2): undefined reference to `nf_get_vara_double_'
collect2: ld returned 1 exit status
hf77: No such file or directory
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2
ptmlxsmp:/usr/local/amber9/src #
Even I have tried without -bintraj, but still error at configure stage as below:
ptmlxsmp:/usr/local/amber9/src # export MKL_LIBRARY=/opt/intel/mkl/10.0.010/lib/64
ptmlxsmp:/usr/local/amber9/src # export MKL_LIB=/opt/intel/mkl/10.0.010/lib/64 ptmlxsmp:/usr/local/amber9/src # ./configure -lam -mmtsb -verbose gfortran AMBERHOME is set to /usr/local/amber9
Setting up Amber configuration file for architecture: gfortran
Using parallel communications library: lam
MPI_HOME is set to /usr/local/lam/
MKL_HOME is set to /opt/intel/mkl/
MKL libraries were not found !
The configuration file, config.h, was successfully created.
ptmlxsmp:/usr/local/amber9/src #
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
--- On Fri, 6/2/09, David A. Case <case.biomaps.rutgers.edu> wrote:
> From: David A. Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] amber9 installation problem in SMP IA64
> To: vjrajamany.yahoo.com, "AMBER Mailing List" <amber.ambermd.org>
> Date: Friday, 6 February, 2009, 9:25 PM
> On Thu, Feb 05, 2009, Vijay Manickam Achari wrote:
> >
> > Here I have posted a problem which I encounter during
> installation of amber9
> >
> > prob in SMP (128cores IA64) for amber9 installation:
> > ../configure -lam -verbose -mmtsb -bintraj gfortran
> > then edit the config.h and changed gfortran to hf77 or
> mpif77
>
> This sounds pretty dangerous. The configure script does a
> netcdf
> configuration using gfortran as the compiler, and when you
> later change
> the compiler, you could end up with incompatible naming
> schemes.
>
> Things to try: first, remove the -bintraj file, and make
> sure that
> everything else is OK. Second, with the -bintraj file back
> there
> (*assuming* that you feel you need this option!) use
> "nm" to examine the
> symbols in $AMBERHOME/src/netcdf/lib/libnetcdf.a: it's
> likely that they
> have more or fewer underscores than in the error messages,
> and you can
> try to piece things together from that. Or, just try to
> re-configure
> netcdf with the compiler you really intend to use.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 11 2009 - 01:15:51 PST
