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
shake.F90:940.132:
tected in equilibrium bond length for',/5x,'SHAKEn TI atoms',1x,i8,2x,i8,2x
1
Error: Unexpected end of format string in format string at (1)
shake.F90:941.132:
nchronized from V0. ',/1x,'Consider using noshake mask or disabling SHAKE.'
1
Error: Unexpected end of format string in format string at (1)
shake.F90:932.41:
if (master) write (mdout, 1111) abs(partner_req - req), i,j,ipartner
1
Error: FORMAT label 1111 at (1) not defined
shake.F90:937.49:
if (master .and. write_msg) write(mdout, 1112)
1
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 ‘-V’
gcc: fatal error: no input files
compilation terminated.
[root.pleiades amber14]# gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.3/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info
--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
--with-linker-hash-style=gnu
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto
--enable-plugin --enable-initfini-array --enable-java-awt=gtk
--disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
--enable-libgcj-multifile --enable-java-maintainer-mode
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar
--disable-libjava-multilib
--with-isl=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/isl-install
--with-cloog=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/cloog-install
--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
healer.rpi.edu
(518) 276-4407
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Received on Thu Nov 20 2014 - 10:00:02 PST
