Marc -
Sorry; caught me on a 3 day vacation :-). For the error messages below you
need to pick up amber 8 bugfix 38 and apply it to the pmemd src (the one c
file there). Read the info on the bugfixes link on amber.scripps.edu, and
pick up the actual bugfix.38 there. I presume you are running opterons
here? At any rate, use the new_configure stuff for pmemd. Regarding
LAM_HOME, I think for pmemd this is something like MPI_HOME now, and it is
an environment variable that is set in the script for pmemd (you would be
asked where the LAM MPI files are installed). For the regular amber script
I think it tells you to set an environment variable named LAM_HOME. This is
something you do manually; from the csh enter:
setenv LAM_HOME <whereever in the heck you installed LAM>. I think it is
possible that lam may be built with gcc, but I am not sure; the safest thing
to do is to build it with pathscale c. Ask more questions on Monday and I
will attempt to refine my answers; I just got back and my actual amber
machines are not up, so these are handwaving answers.
Regards - Bob Duke
----- Original Message -----
From: "Marc Petitmermet" <petitmermet.mat.ethz.ch>
To: <amber.scripps.edu>
Sent: Thursday, March 31, 2005 10:32 AM
Subject: AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS
> 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
> http://amber.scripps.edu/pmemd-mar05.html 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.
>
> Regards,
> Marc
>
>
>
> 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
> `STOP_LOADBAL_TIMER.in.PARALLEL_DAT_MODULE':
> : undefined reference to `get_wall_time__'
> parallel_dat.o(.text+0x10dd): In function
> `START_LOADBAL_TIMER.in.PARALLEL_DAT_MODULE':
> : undefined reference to `get_wall_time__'
> prmtop_dat.o(.text+0x7f6e): In function
> `BCAST_PRMTOP_DAT.in.PRMTOP_DAT_MODULE':
> : undefined reference to `get_bytesize__'
> prmtop_dat.o(.text+0x7fef): In function
> `BCAST_PRMTOP_DAT.in.PRMTOP_DAT_MODULE':
> : undefined reference to `get_bytesize__'
> prmtop_dat.o(.text+0x8071): In function
> `BCAST_PRMTOP_DAT.in.PRMTOP_DAT_MODULE':
> : undefined reference to `get_bytesize__'
> runmin_cit.o(.text+0x67c9): In function `PRINTE.in.RUNMIN_CIT_MODULE':
> : undefined reference to `get_wall_time__'
> runmin_cit.o(.text+0x6f46): In function `PRINTE.in.RUNMIN_CIT_MODULE':
> : undefined reference to `get_wall_time__'
> runfiles.o(.text+0x5e32): In function `PRNTMD.in.RUNFILES_MODULE':
> : undefined reference to `get_wall_time__'
> runfiles.o(.text+0x69ad): In function `PRNTMD.in.RUNFILES_MODULE':
> : 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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 03 2005 - 03:53:02 PDT
