[AMBER] Errors compiling Amber 14 after applying update 7

From: Bob Healey <healer.rpi.edu>
Date: Thu, 20 Nov 2014 12:45:08 -0500

Just got my Amber license this week, unpacked everything and started
compiling according to the manual. The first pass through (./configure
gnu && make install) applied up to update 6. When I went to do the MPI
build, the update script found update 7. After applying it, I can not
get the compilation to complete. I even deleted my source tree and
started over a few times. Before I roll back to update 6, I was
wondering if anyone on this list had any advice for me. I am using
Fedora 19, with stock compilers.

Thank you.

gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native
-I/usr/local/amber/amber14/include -c shake.F90

tected in equilibrium bond length for',/5x,'SHAKEn TI atoms',1x,i8,2x,i8,2x
Error: Unexpected end of format string in format string at (1)

nchronized from V0. ',/1x,'Consider using noshake mask or disabling SHAKE.'
Error: Unexpected end of format string in format string at (1)

if (master) write (mdout, 1111) abs(partner_req - req), i,j,ipartner
Error: FORMAT label 1111 at (1) not defined

if (master .and. write_msg) write(mdout, 1112)
Error: FORMAT label 1112 at (1) not defined
make[3]: *** [shake.o] Error 1
make[3]: Leaving directory `/usr/local/amber/amber14/src/pmemd/src'
make[2]: *** [serial] Error 2
make[2]: Leaving directory `/usr/local/amber/amber14/src/pmemd'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/usr/local/amber/amber14/src'
make: *** [install] Error 2
[root.pleiades amber14]# gcc -V
gcc: error: unrecognized command line option ā€˜-Vā€™
gcc: fatal error: no input files
compilation terminated.
[root.pleiades amber14]# gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
--enable-shared --enable-threads=posix --enable-checking=release
--with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions
--enable-gnu-unique-object --enable-linker-build-id
--enable-plugin --enable-initfini-array --enable-java-awt=gtk
--disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-
--enable-libgcj-multifile --enable-java-maintainer-mode
--with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.3 20140911 (Red Hat 4.8.3-7) (GCC)

Bob Healey
Systems Administrator
Biocomputation and Bioinformatics Constellation
and Molecularium
(518) 276-4407
AMBER mailing list
Received on Thu Nov 20 2014 - 10:00:02 PST
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