RE: amber-developers: Two build/test issues from Lachele Foley on 2008-11-03 (Amber Developers Archive Nov 2008)

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Mon, 03 Nov 2008 16:52:59 -0500
[root.keats ~]# gfortran -v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: /scratch2/installer_storage/gcc-4.2.3/configure
Thread model: posix
gcc version 4.2.3

:-) Lachele
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Ross Walker
[mailto:ross.rosswalker.co.uk]
To: amber-developers.scripps.edu
Sent: Mon,
03 Nov 2008 16:45:04 -0500
Subject: RE: amber-developers: Two build/test
issues
> Hi Lachele,
> 
> One quick thing - what version of gfortran are you using?
> 
> gfortran -v
> 
> All the best
> Ross
> 
> > -----Original Message-----
> > From: owner-amber-developers.scripps.edu [mailto:owner-amber-
> > developers.scripps.edu] On Behalf Of Lachele Foley
> > Sent: Monday, November 03, 2008 11:58 AM
> > To: amber-developers.scripps.edu
> > Subject: amber-developers: Two build/test issues
> > 
> > The actual problems are near the end, and plainly marked, but I'm
> > including other info because I figure you'll want it.  I fear I've
> > neglected some critical step, but I can't see it.  If not, then here are a
> > couple issues for you.  If so, apologies in advance...
> > 
> > 
> > keats:src>echo $AMBERHOME
> > /usr/local/programs/amber11
> > 
> > keats:src>pwd
> > /usr/local/programs/amber11/src
> > 
> > keats:src>echo $MPI_HOME
> > /opt/scali
> > 
> > keats:src>echo $PATH
> > <snip>:/usr/local/programs/amber11/exe:<snip>
> > <no other amber in path>
> > 
> > keats:src>./configure_at gcc
> > <snip>
> > The configuration file, config.h, was successfully created.
> > <snip>
> > 
> > keats:src>make -f Makefile_at
> > <snip>
> > Installation of AmberTools, version 1.2 is complete at Mon Nov  3 14:01:06
> > EST 2008.
> > 
> > keats:src>cd ../test ; make -f Makefile_at test
> > <snip>
> > Finished test suite for AmberTools
> > keats:test>mv TEST_FAILURES.diff AmberTools_TEST_FAILURES.diff
> > keats:test>more AmberTools_TEST_FAILURES.diff
> > <looks normal>
> > 
> > keats:test>make -f Makefile_at  clean
> > keats:test>cd ../src ; make -f Makefile_at clean
> > 
> > keats:src>./configure_amber gfortran
> > <snip>
> > The configuration file, config_amber.h, was successfully created.
> > 
> > keats:src>make serial
> > <snip>
> > Installation of Amber11 (serial) is complete at Mon Nov  3 14:17:56 EST
> > 2008.
> > 
> > 
> > ==========================
> > The first issue
> > ==========================
> > keats:src>cd ../test ; make test
> > <snip>
> > cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb1
> > Segmentation fault
> >   ./Run.nma_md_qmgb1:  Program error
> > make: *** [test.sander.QMMM.nopar] Error 1
> > 
> > keats:test>cp TEST_FAILURES.diff Serial_TEST_FAILURES.diff
> > 
> > keats:test>cd ../src/ ; make clean
> > keats:src>./configure_amber -scali gfortran
> > <snip>
> > The configuration file, config_amber.h, was successfully created.
> > 
> > keats:src>make clean
> > <again just for good measure>
> > 
> > 
> > ==========================
> > The second issue
> > ==========================
> > keats:src>make parallel
> > <snip>
> > cp ../netcdf/include/*.mod .
> > cp ../netcdf/bin/ncdump ../../exe
> > touch netcdf.o
> > cpp -traditional -I/opt/scali/include -P -xassembler-with-cpp -
> > Dsecond=ambsecond -DBINTRAJ -DMPI  ncsu-umbrella.f > _ncsu-umbrella.f
> > gfortran -c -O3 -fno-second-underscore -ffree-form  -o ncsu-umbrella.o
> > _ncsu-umbrella.f
> > cpp -traditional -I/opt/scali/include -P -xassembler-with-cpp -
> > Dsecond=ambsecond -DBINTRAJ -DMPI  ncsu-abmd-hooks.f > _ncsu-abmd-hooks
> > .f
> > gfortran -c -O3 -fno-second-underscore -ffree-form  -o ncsu-abmd-hooks.o
> > _ncsu-abmd-hooks.f
> > cpp -traditional -I/opt/scali/include -P -xassembler-with-cpp -
> > Dsecond=ambsecond -DBINTRAJ -DMPI  ncsu-smd-hooks.f > _ncsu-smd-hooks.f
> > gfortran -c -O3 -fno-second-underscore -ffree-form  -o ncsu-smd-hooks.o
> > _ncsu-smd-hooks.f
> > cpp -traditional -I/opt/scali/include -P -xassembler-with-cpp -
> > Dsecond=ambsecond -DBINTRAJ -DMPI  mt19937.f > _mt19937.f
> > gfortran -c -O0 -fno-second-underscore -ffree-form  -o mt19937.o
> > _mt19937.f
> > _mt19937.f:324.30:
> > 
> >     data temper_b /z'EFC60000'/
> >                              1
> > Error: Arithmetic overflow converting INTEGER(8) to INTEGER(4) at (1)
> > _mt19937.f:323.30:
> > 
> >     data temper_a /z'9D2C5680'/
> >                              1
> > Error: Arithmetic overflow converting INTEGER(8) to INTEGER(4) at (1)
> > _mt19937.f:321.30:
> > 
> >     data matrix_a /z'9908B0DF'/
> >                              1
> > Error: Arithmetic overflow converting INTEGER(8) to INTEGER(4) at (1)
> > _mt19937.f:271.28:
> > 
> >     data msb1_d /z'80000000'/
> >                            1
> > Error: Arithmetic overflow converting INTEGER(8) to INTEGER(4) at (1)
> > make[1]: *** [mt19937.o] Error 1
> > make[1]: Leaving directory `/usr/local/programs/amber11/src/sander'
> > make: *** [parallel] Error 2
> > keats:src>
> > 
> > 
> > 
> > 
> > 
> > :-) Lachele
> > --
> > B. Lachele Foley, PhD '92,'02
> > Assistant Research Scientist
> > Complex Carbohydrate Research Center, UGA
> > 706-542-0263
> > lfoley.ccrc.uga.edu
> 
>
Received on Fri Dec 05 2008 - 10:34:08 PST