AMBER Archive (2008)

Subject: Re: AMBER: amber10 installation problem

From: Robert Duke (
Date: Tue Jun 10 2008 - 17:02:54 CDT

Read the README in the pmemd directory about handling mpich configuration
problems. You probably need to execute a 'mpif77 -link_info' command on
your system to see exactly what libraries are needed for your mvapich
implementation, and where they are located. You then modify the appropriate
pieces of the first approximate config.h that you have. It is pretty hard
to get all this stuff right with different OS's and different versions of
the different mpi implementations. In an ideal world, pmemd would by
issuing the 'mpif77 -link_info' itself and extracting the necessary info,
but that unfortunately does not work at all installations either (so there
is a problem with the diversity of things we can see at various
supercomputer installations). Anyway, try the above, and let me know how
much further you get.
Regards - Bob Duke

----- Original Message -----
From: "Ed Pate" <>
To: <>
Sent: Tuesday, June 10, 2008 4:59 PM
Subject: AMBER: amber10 installation problem

> Dear Amber Community:
> We are trying to install the parallel version of pmemd in Amber10, without
> success.
> Our system is is opteron, 64 bit. pgf90 fortran. The os is Suse10.0.
> There are infiniband interconnects and mpich 1.2.7
> configure: --with-device=ch_gen2 --with-arch=LINUX -prefix=/usr/local/mvapich-pgi
> --with-romio --without-mpe -lib=-L/usr/ofed/lib64 -Wl,-rpath=/usr/ofed/lib64
> -libverbs -lpthread
> MPICH Device: ch_gen2
> The configure command is
> configure linux64_opteron pgf90 mvapich
> We appear to get a successful generation of the makefile (after answering
> two questions re: mvapich location and infiniband location).
> The "make" command output ends with the following error message:
> /usr/bin/ld: cannot find -lmtl_common
> make[1]: *** [pmemd] Error 2
> make[1]: Leaving directory `/usr/local/amber10/amber10/src/pmemd/src'
> make: *** [all] Error 2
> We have looked and cannot find libmtl_common*
> We would appreciate it if anyone could point us in the right direction.
> Thanks
> Ed Pate
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