Dear Dr. Case and All,
Thanks for your advice. I tried to install amber10 on another computer:
starbuck /opt# uname -a
Linux starbuck 2.6.19-ck2-suse102-osmp #1 SMP Thu Feb 8 15:16:20 EST
2007 x86_64 x86_64 x86_64 GNU/Linux
The following are what I did and the compiling message - a confusing
problem with step of "make parallel":
1. unpacked both Amber10.tar & AmberTools-1.2.tar at /opt/amber10
2. setenv AMBERHOME /opt/amber10, and added set PATH = ( $PATH
/opt/amber10/bin )
3. patch -p0 -N -r patch-rejects < bugfix.all
4. starbuck amber10/src# ./configure_amber -lamsource gfortran
-> The configuration file, config_amber.h, was successfully created.
5. ./configure_lam
--> LAM/MPI 7.1.3 has been built.
Installation of LAM/MPI 7.1.3 is complete.
6. starbuck amber10/src# make parallel
Starting installation of Amber10 (parallel) at Tue Jan 6 09:50:41 EST 2009.
cd sander; make parallel
make[1]: Entering directory `/usr/opt/amber10/src/sander'
./checkparconf
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI constants.f > _constants.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o constants.o _constants.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI nose_hoover.f > _nose_hoover.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o nose_hoover.o _nose_hoover.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI nose_hoover_vars.f >
_nose_hoover_vars.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o nose_hoover_vars.o _nose_hoover_vars.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI pimd_vars.f > _pimd_vars.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o pimd_vars.o _pimd_vars.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI cmd_vars.f > _cmd_vars.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o cmd_vars.o _cmd_vars.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI nose_hoover_init.f >
_nose_hoover_init.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o nose_hoover_init.o _nose_hoover_init.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI stack.f > _stack.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o stack.o _stack.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI findmask.f > _findmask.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o findmask.o _findmask.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI qmmm_module.f > _qmmm_module.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o qmmm_module.o _qmmm_module.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI qm2_dftb_module.f >
_qm2_dftb_module.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o qm2_dftb_module.o _qm2_dftb_module.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI trace.f > _trace.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o trace.o _trace.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI lmod.f > _lmod.f
/opt/amber10/bin/mpif77 -c -O0 -fno-range-check -fno-second-underscore
-ffree-form -o lmod.o _lmod.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI parms.f > _parms.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o parms.o _parms.f
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI softcore.f > _softcore.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o softcore.o _softcore.f
In file _softcore.f:899
write (6,'(a,i5,a)') ' Molecule ',imol,' is
nonsoftcore, but
1
Error: Unterminated character constant beginning at (1)
/opt/amber10/bin/mpif77: No such file or directory
make[1]: *** [softcore.o] Error 1
make[1]: Leaving directory `/usr/opt/amber10/src/sander'
make: *** [parallel] Error 2
resultant files in amber10/bin:
starbuck amber10/bin# ls -l
total 3577
-rwxr-xr-x 1 root root 62445 2009-01-06 11:25 hboot
lrwxrwxrwx 1 root root 5 2009-01-06 11:25 hcc -> mpicc
lrwxrwxrwx 1 root root 5 2009-01-06 11:25 hcp -> mpiCC
lrwxrwxrwx 1 root root 6 2009-01-06 11:25 hf77 -> mpif77
-rwxr-xr-x 1 root root 194474 2009-01-06 11:25 lamboot
-rwxr-xr-x 1 root root 170819 2009-01-06 11:25 lamcheckpoint
-rwxr-xr-x 1 root root 99990 2009-01-06 11:25 lamclean
-rwxr-xr-x 1 root root 280842 2009-01-06 11:25 lamd
-rwxr-xr-x 1 root root 124152 2009-01-06 11:25 lamexec
-rwxr-xr-x 1 root root 210535 2009-01-06 11:25 lamgrow
-rwxr-xr-x 1 root root 89938 2009-01-06 11:25 lamhalt
-rwxr-xr-x 1 root root 698998 2009-01-06 11:25 laminfo
-rwxr-xr-x 1 root root 94986 2009-01-06 11:25 lamnodes
-rwxr-xr-x 1 root root 170816 2009-01-06 11:25 lamrestart
-rwxr-xr-x 1 root root 99665 2009-01-06 11:25 lamshrink
-rwxr-xr-x 1 root root 99368 2009-01-06 11:25 lamtrace
-rwxr-xr-x 1 root root 194194 2009-01-06 11:25 lamwipe
-rwxr-xr-x 1 root root 61509 2009-01-06 11:25 mpic++
-rwxr-xr-x 1 root root 61506 2009-01-06 11:25 mpicc
lrwxrwxrwx 1 root root 6 2009-01-06 11:25 mpiCC -> mpic++
-rwxr-xr-x 1 root root 19941 2009-01-06 11:25 mpiexec
-rwxr-xr-x 1 root root 61509 2009-01-06 11:25 mpif77
-rwxr-xr-x 1 root root 118025 2009-01-06 11:25 mpimsg
-rwxr-xr-x 1 root root 228654 2009-01-06 11:25 mpirun
-rwxr-xr-x 1 root root 117102 2009-01-06 11:25 mpitask
-rwxr-xr-x 1 root root 189929 2009-01-06 11:25 recon
-rwxr-xr-x 1 root root 57651 2009-01-06 11:25 tkill
-rwxr-xr-x 1 root root 99073 2009-01-06 11:25 tping
lrwxrwxrwx 1 root root 7 2009-01-06 11:25 wipe -> lamwipe
I was hoping that you could help me.
Thank you!
Wen
Quoting "David A. Case" <case.biomaps.rutgers.edu>:
> On Wed, Dec 31, 2008, wl2290.columbia.edu wrote:
>>
>> First, here is the version of g++/gcc on my computer:
>>
>> gcc -v --> gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)
>>
>> About g95 on my computer:
>> gcc version 4.0.3 (g95 0.92!) Nov 18 2008
>
> I suppose its possible that lam is getting confused by the fact that g95
> that uses gcc 4.0.3 vs the 4.1.2 version that is really installed.
> Since you apparently have gfortran already installed, why not configure
> with that?
>
> ./configure_amber -lamsource gfortran
>
> It's at least worth a try.
>
> There's a old discussion of something like this here:
>
> http://www.lam-mpi.org/MailArchives/lam/2006/05/12357.php
>
> but in that case, lam recognized that it was using g++. I'm still puzzled
> by the log file saying that lam was not using g++. All of these suggest,
> though, that there is something odd/broken with your compilers. Do you
> have access to some other machine to see if the problem might be localized
> to one installation?
>
> ...dac
>
>
>
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Received on Tue Jan 06 2009 - 15:31:25 PST
