[AMBER] Errors in Amber12 installation

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Mon, 8 Oct 2012 14:28:04 -0400

Hi all,

I am trying to install Amber12. I am trying to install it first serial and
then parallel.

So I am typing following commands in the amber12 directory

./configure pgi>& config_serial.log &

Here is my config_serial.log

Checking for updates...
AmberTools13 is up to date
Amber13 is up to date

Searching for python2... Found python2.7: /usr/local/bin/python2.7

Obtaining the PGI suite version:
      pgcc -V
The version is 12.6-0

Testing the pgcc compiler:
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK

Testing the pgf90 compiler:
     pgf90 -O1 -o testp testp.f
OK

Testing mixed C/Fortran compilation:
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
     pgf90 -O1 -c -o testp.f.o testp.f
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
testp.f.o -pgf90libs
OK

Testing pointer size:
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
test_pointer_size.c
Detected 64 bit operating system.

Testing flex: OK

Configuring NetCDF (may be time-consuming)...

    NetCDF configure succeeded.

Checking for zlib: OK

Checking for libbz2: PGC-F-0206-Can't find include file bzlib.h (testp.c: 2)
PGC/x86-64 Linux 12.6-0: compilation aborted
./configure2: line 1884: ./testp: No such file or directory
Not found.

Configuring fftw-3.3 (may be time-consuming)...

    fftw-3.3 configure succeeded.

Configuring XBLAS (may be time-consuming)...

    XBLAS configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type 'make install'

Cleaning the src directories. This may take a few moments.
Configure complete.

Now I type

make install >& make_serial.log &

I have attached my make_serial.log file (It is sooo big). But the lines
that give the errors are

pgf90 -DBINTRAJ -I/wsu/home/ej/ej02/ej0271/amber12/include
-I/wsu/home/ej/ej02/ej0271/amber12/include -o calcpka calcpka.F90
pgf90-Fatal-/wsu/usr/pgi/linux86-64_2.6/12.6/bin/pgf901 TERMINATED by
signal 11
Arguments to /wsu/usr/pgi/linux86-64_2.6/12.6/bin/pgf901
/wsu/usr/pgi/linux86-64_2.6/12.6/bin/pgf901 calcpka.F90 -opt 1 -terse 1
-inform warn -nohpf -nostatic -x 19 0x400000 -quad -x 59 4 -x 59 4 -x 15 2
-x 49 0x400004 -x 51 0x20 -x 57 0x4c -x 58 0x10000 -x 124 0x1000 -x 57
0xfb0000 -x 58 0x78031040 -x 48 4608 -x 49 0x100 -x 120 0x200 -stdinc
/wsu/usr/pgi/linux86-64_2.6/12.6/include:/usr/local/include:/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include:/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include:/usr/include
-def unix -def __unix -def __unix__ -def linux -def __linux -def __linux__
-def __NO_MATH_INLINES -def __x86_64 -def __x86_64__ -def
__LONG_MAX__=9223372036854775807L -def '__SIZE_TYPE__=unsigned long int'
-def '__PTRDIFF_TYPE__=long int' -def __THROW= -def __extension__= -def
__amd_64__amd64__ -def __k8 -def __k8__ -def __SSE__ -def __MMX__ -def
__SSE2__ -def __SSE3__ -def __SSSE3__ -idir
/wsu/home/ej/ej02/ej0271/amber12/include -idir
/wsu/home/ej/ej02/ej0271/amber12/include -def BINTRAJ -preprocess -freeform
-vect 48 -y 54 1 -modexport /tmp/pbs.307301.vpbs1/pgf90Tmdfhhwt3A5R.cmod
-modindex /tmp/pbs.307301.vpbs1/pgf90vmdf--MyIXVj.cmdx -output
/tmp/pbs.307301.vpbs1/pgf90fmdfpDIyvyCD.ilm
make[2]: *** [calcpka] Error 127
make[2]: Leaving directory
`/wsu/home/ej/ej02/ej0271/amber12/AmberTools/src/etc'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/wsu/home/ej/ej02/ej0271/amber12/AmberTools/src'
make: *** [install] Error 2

I don't know why this error is given. Could anyone please give me
suggestions to fix this error?

Thank you

Sajeewa Dewage


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Received on Mon Oct 08 2012 - 11:30:07 PDT
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