AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS

From: Marc Petitmermet <>
Date: Thu, 31 Mar 2005 17:32:31 +0200

Dear List Members

Robert Duke suggested to have a look at the pathscale 2.1 compiler to
get amber8 running. Now I have a temporary license but am a little bit
lost. The configure script does not support this compiler out-of-the
box and I have zero experience with fortran and mapi/lam/etc. On RHEL 4
AS there is not a LAM_HOME; part of the lam package is in /usr/lib64,
/usr/include, /usr/include/mpi2cxx. This means some manual configuring
in config.h...

I then thought that I can learn something from Robert's new scripts at and only compile pmemd to
start with. But this results in the error shown below.

Then I tried to compile leap on it's own as somebody in the mailing
list said that this is fairly easy. Here I had to change Line 114 of
$AMBERHOME/src/leap/src/leap/Makefile to "lib64" from "lib" (Lee
Shekter). Now it compiles with warnings. But the xleap and xaleap quit
upon start with a segmentation fault.

Well, any help is much appreciated.


pathf90 -o pmemd gbl_constants.o gbl_datatypes.o file_io_dat.o
parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o
inpcrd_dat.o gbl_dat.o ew_dat.o ew_direct_cit_dat.o ew_direct_cit.o
ew_recip_cit.o ew_fft_cit.o ew_force_cit.o ew_bspline.o ew_box.o
ew_pairlist.o force_cit.o runmd_cit.o shake_cit.o runmin_cit.o
axis_optimize_cit.o ew_lib.o pmemd_lib.o runfiles.o file_io.o
pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o
get_cmdline.o master_setup.o alltasks_setup.o ew_setup.o
nextprmtop_section.o -L/usr/lib64 -llamf77mpi -lmpi -llam -ldl
-lpthread -Wl,-rpath=/opt/pathscale/lib/2.1:/opt/pathscale/lib/2.1/32:
parallel_dat.o(.text+0x10fb): In function
: undefined reference to `get_wall_time__'
parallel_dat.o(.text+0x10dd): In function
: undefined reference to `get_wall_time__'
prmtop_dat.o(.text+0x7f6e): In function
: undefined reference to `get_bytesize__'
prmtop_dat.o(.text+0x7fef): In function
: undefined reference to `get_bytesize__'
prmtop_dat.o(.text+0x8071): In function
: undefined reference to `get_bytesize__'
runmin_cit.o(.text+0x67c9): In function `':
: undefined reference to `get_wall_time__'
runmin_cit.o(.text+0x6f46): In function `':
: undefined reference to `get_wall_time__'
runfiles.o(.text+0x5e32): In function `':
: undefined reference to `get_wall_time__'
runfiles.o(.text+0x69ad): In function `':
: undefined reference to `get_wall_time__'
collect2: ld returned 1 exit status
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/usr/local/amber8/src/pmemd/src'
make: *** [install] Error 2

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Received on Thu Mar 31 2005 - 16:53:00 PST
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