There's no rule for distclean in Makefile in $AMBERHOME, only make clean.
But that would remove everything from the serial build, and also, this
error I have is the same error that happens when you run make install after
a -mpi config without the serial build first, so it couldn't be a problem
with old files.
On Sat, Jan 14, 2017 at 11:07 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Did you "make distclean" before retrying yet? (leftover files cause messy
> sometimes).
> Even better, try AmberTools16: http://ambermd.org/AmberTools16-get.html
>
> Hai
>
> On Sat, Jan 14, 2017 at 10:22 AM, Ada Sedova <ada.a.sedova.gmail.com>
> wrote:
>
> > *Just tried rebuilding serial and then parallel in the same folder, one
> > after the other, as instructed.*
> >
> > **The yacc/cifparse error is still crashing the build:**
> >
> > *stdout:*
> >
> > make[2]: Entering directory
> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cifparse'
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc -v -d cifparse.y
> >
> > make[2]: *** [cifp.tab.c] Error 1
> >
> > make[1]: *** [parallel] Error 2
> >
> > make: *** [install] Error 2
> >
> > make[2]: Leaving directory
> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cifparse'
> >
> > make[1]: Leaving directory
> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src'
> >
> >
> > *stderr:*
> >
> > yacc:22340 terminated with signal 11 at PC=40abac SP=7ffce7b14400.
> > Backtrace:
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x40abac]
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x40ce6b]
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x404dfd]
> >
> > /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f773ecc1d1d]
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x400ea9]
> >
> > make[2]: *** [cifp.tab.c] Error 1
> >
> > make[1]: *** [parallel] Error 2
> >
> > make: *** [install] Error 2
> >
> >
> > *compilers:*
> >
> > PE-gnu/4.8.2-1.8.4
> >
> > openmpi/1.8.4
> >
> >
> > *output from ./config:*
> >
> > Obtaining the gnu suite version:
> >
> > gcc -v
> >
> > The version is 4.8.2
> >
> >
> > Testing the gcc compiler:
> >
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> >
> > OK
> >
> >
> > Testing the g++ compiler:
> >
> > g++ -o testp testp.cpp
> >
> > OK
> >
> >
> > Testing the gfortran compiler:
> >
> > gfortran -O0 -o testp testp.f
> >
> > OK
> >
> >
> > Testing mixed C/Fortran compilation:
> >
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> > testp.c
> >
> > gfortran -O0 -c -o testp.f.o testp.f
> >
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> > testp.f.o -lgfortran -w
> >
> > OK
> >
> >
> > Testing pointer size:
> >
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
> test_pointer_size
> > test_pointer_size.c
> >
> > Detected 64 bit operating system.
> >
> >
> > Testing flex: OK
> >
> >
> > Checking NetCDF...
> >
> > Using bundled NetCDF library.
> >
> > Using existing NetCDF in '/ccs/home/adaa/AMBER/amber14'
> >
> > Checking NetCDF...
> >
> > Using bundled NetCDF library.
> >
> > Using existing NetCDF in '/ccs/home/adaa/AMBER/amber14'
> >
> >
> > Checking for zlib: OK
> >
> >
> > Checking for libbz2: OK
> >
> >
> > Configuring fftw-3.3 for mdgx (may be time-consuming)...
> >
> >
> > fftw-3.3 configure succeeded.
> >
> > testing [C++ / fortran] cross-compile with MPI libs
> >
> > The configuration file, config.h, was successfully created.
> >
> >
> >
> > *mpicc and mpif90:*
> >
> > -bash-4.1$ mpicc -show
> >
> > gcc -I/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/include -pthread
> > -L/usr/lib64
> > -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath
> > -Wl,/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib -Wl,--enable-new-dtags
> > -L/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib -lmpi
> >
> > -bash-4.1$ mpif90 -show
> >
> > gfortran -I/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/include -pthread
> > -I/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib -L/usr/lib64 -Wl,-rpath
> > -Wl,/usr/lib64 -Wl,-rpath -Wl,/sw/rhea/openmpi/1.8.4/
> rhel6.6_gcc4.8.2/lib
> > -Wl,--enable-new-dtags -L/sw/rhea/openmpi/1.8.4/rhel6.6_gcc4.8.2/lib
> > -lmpi_usempi -lmpi_mpifh -lmpi
> >
> >
> > *redhat version:*
> >
> > -bash-4.1$ cat /etc/redhat-release
> >
> > Red Hat Enterprise Linux Server release 6.8 (Santiago)
> >
> > On Sat, Jan 14, 2017 at 9:22 AM, Ada Sedova <ada.a.sedova.gmail.com>
> > wrote:
> >
> > > Great, thanks. I'm going to see what it's going to take to get OLCF a
> > site
> > > license upgrade to 16 next week.
> > >
> > > What about #1? Should I track this down and change all to MAP_LABEL?
> > >
> > > On Sat, Jan 14, 2017 at 12:07 AM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
> > >
> > >> per 2-4: it's ok to ignore. The GB energies are fine, but the reported
> > >> parameters in mdout are not correct (updated in amber16).
> > >> (likely related to: http://archive.ambermd.org/201602/0190.html)
> > >>
> > >> Hai
> > >>
> > >> On Fri, Jan 13, 2017 at 11:22 PM, Ada Sedova <ada.a.sedova.gmail.com>
> > >> wrote:
> > >>
> > >> > THANK YOU!
> > >> >
> > >> > *As for the tests, they did all pass in terms of errors, but there
> > were
> > >> > four diffs in Amber:*
> > >> >
> > >> > make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/
> > >> > AMBER/amber14/test'
> > >> >
> > >> > 148 file comparisons passed
> > >> >
> > >> > 4 file comparisons failed
> > >> >
> > >> > 0 tests experienced errors
> > >> >
> > >> > 1)
> > >> > This one looks like a typo unless you really have two different
> > >> variables
> > >> > one named MAPLABLE and one named MAPLABEL
> > >> >
> > >> > * MAPLABLE = EMAP
> > >> >
> > >> > *
> > >> >
> > >> > *> MAPLABEL = EMAP *
> > >> >
> > >> >
> > >> > The others I am unsure:
> > >> >
> > >> > 2-4)
> > >> >
> > >> > possible FAILURE: check mdout.trxox.dif
> > >> >
> > >> >
> > >> >
> > >> > /ccs/home/adaa/AMBER/amber14/test/gb8_trx
> > >> >
> > >> >
> > >> >
> > >> > 46a47,51
> > >> >
> > >> > *> gb_alpha_hnu = 0.53705, gb_beta_hnu = 0.36286,
> > >> > gb_gamma_hnu = 0.11670
> > >> > *
> > >> >
> > >> > *> gb_alpha_cnu = 0.33167, gb_beta_cnu = 0.19684,
> > >> > gb_gamma_cnu = 0.09342
> > >> > *
> > >> >
> > >> > *> gb_alpha_nnu = 0.68631, gb_beta_nnu = 0.46319,
> > >> > gb_gamma_nnu = 0.13872
> > >> > *
> > >> >
> > >> > *> gb_alpha_onu = 0.60634, gb_beta_onu = 0.46301,
> > >> > gb_gamma_onu = 0.14226
> > >> > *
> > >> >
> > >> > *> gb_alpha_pnu = 0.41836, gb_beta_pnu = 0.29005,
> > >> > gb_gamma_pnu = 0.10642
> > >> > *
> > >> >
> > >> > *---------------------------------------
> > >> >
> > >> > *
> > >> >
> > >> > possible FAILURE: check mdout.trxox_md.dif
> > >> >
> > >> >
> > >> >
> > >> > /ccs/home/adaa/AMBER/amber14/test/gb8_trx
> > >> >
> > >> >
> > >> >
> > >> > 48a49,53
> > >> >
> > >> > *> gb_alpha_hnu = 0.53705, gb_beta_hnu = 0.36286,
> > >> > gb_gamma_hnu = 0.11670
> > >> > *
> > >> >
> > >> > *> gb_alpha_cnu = 0.33167, gb_beta_cnu = 0.19684,
> > >> > gb_gamma_cnu = 0.09342
> > >> > *
> > >> >
> > >> > *> gb_alpha_nnu = 0.68631, gb_beta_nnu = 0.46319,
> > >> > gb_gamma_nnu = 0.13872
> > >> > *
> > >> >
> > >> > *> gb_alpha_onu = 0.60634, gb_beta_onu = 0.46301,
> > >> > gb_gamma_onu = 0.14226
> > >> > *
> > >> >
> > >> > *> gb_alpha_pnu = 0.41836, gb_beta_pnu = 0.29005,
> > >> > gb_gamma_pnu = 0.10642
> > >> > *
> > >> >
> > >> > *---------------------------------------
> > >> >
> > >> > *
> > >> >
> > >> > possible FAILURE: check mdout.trxox_md.dif
> > >> >
> > >> >
> > >> >
> > >> > /ccs/home/adaa/AMBER/amber14/test/gb8_trx
> > >> >
> > >> >
> > >> >
> > >> > 48a49,53
> > >> >
> > >> > *> gb_alpha_hnu = 0.53705, gb_beta_hnu = 0.36286,
> > >> > gb_gamma_hnu = 0.11670
> > >> > *
> > >> >
> > >> > *> gb_alpha_cnu = 0.33167, gb_beta_cnu = 0.19684,
> > >> > gb_gamma_cnu = 0.09342
> > >> > *
> > >> >
> > >> > *> gb_alpha_nnu = 0.68631, gb_beta_nnu = 0.46319,
> > >> > gb_gamma_nnu = 0.13872
> > >> > *
> > >> >
> > >> > *> gb_alpha_onu = 0.60634, gb_beta_onu = 0.46301,
> > >> > gb_gamma_onu = 0.14226
> > >> > *
> > >> >
> > >> > *> gb_alpha_pnu = 0.41836, gb_beta_pnu = 0.29005,
> > >> > gb_gamma_pnu = 0.10642 *
> > >> >
> > >> >
> > >> > *For AmberTools there are no diff files generated.*
> > >> >
> > >> > I have only the logfile and here is tail:
> > >> >
> > >> > make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/
> > >> > AMBER/amber14/test'
> > >> >
> > >> > make[2]: Entering directory
> > >> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/test'
> > >> >
> > >> >
> > >> > Finished test suite for AmberTools at Fri Jan 13 00:56:46 EST 2017.
> > >> >
> > >> >
> > >> > make[2]: Leaving directory
> > >> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/test'
> > >> >
> > >> > 1271 file comparisons passed
> > >> >
> > >> > 0 file comparisons failed
> > >> >
> > >> > 0 tests experienced errors
> > >> >
> > >> > Test log file saved as
> > >> > /ccs/home/adaa/AMBER/amber14/logs/test_at_serial/2017-01-12_
> > >> 23-29-48.log
> > >> >
> > >> > No test diffs to save!
> > >> >
> > >> >
> > >> > Should these be a problem?
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > On Fri, Jan 13, 2017 at 3:34 PM, Hai Nguyen <nhai.qn.gmail.com>
> > wrote:
> > >> >
> > >> > > On Fri, Jan 13, 2017 at 3:29 PM, Ada Sedova <
> ada.a.sedova.gmail.com
> > >
> > >> > > wrote:
> > >> > >
> > >> > > > So are you saying that the parallel build uses files created in
> > the
> > >> > > serial
> > >> > > > build?
> > >> > >
> > >> > >
> > >> > > Yes. I think the manual should use "MUST" :D.
> > >> > >
> > >> > > This issue happened several times in amber mail list, so I think
> we
> > >> > should
> > >> > > probably add some checking
> > >> > > to make sure user do the serial build first.
> > >> > >
> > >> > > http://dev-archive.ambermd.org/201612/0000.html
> > >> > >
> > >> > > Hai
> > >> > >
> > >> > >
> > >> > > > It was ambiguous in the tutorial why they want you to do the
> > serial
> > >> > > > build first. I assumed it was just so you know what errors
> happen
> > in
> > >> > each
> > >> > > > version.
> > >> > > >
> > >> > > > On Fri, Jan 13, 2017 at 3:26 PM, Hai Nguyen <nhai.qn.gmail.com>
> > >> wrote:
> > >> > > >
> > >> > > > > You told "I have the serial build in a completely different
> > >> folder"
> > >> > > > >
> > >> > > > > What do you mean here?
> > >> > > > >
> > >> > > > > Hai
> > >> > > > >
> > >> > > > > On Fri, Jan 13, 2017 at 3:25 PM, Ada Sedova <
> > >> ada.a.sedova.gmail.com>
> > >> > > > > wrote:
> > >> > > > >
> > >> > > > > > I already did the serial build first, as in my previous
> email.
> > >> > > > > >
> > >> > > > > > On Fri, Jan 13, 2017 at 3:23 PM, Hai Nguyen <
> > nhai.qn.gmail.com>
> > >> > > wrote:
> > >> > > > > >
> > >> > > > > > > Hi
> > >> > > > > > >
> > >> > > > > > > > I have the serial build in a completely different
> folder,
> > >> and I
> > >> > > ran
> > >> > > > > the
> > >> > > > > > > parallel build complete anew, from a different login,
> even.
> > >> > > > > > >
> > >> > > > > > > Try to do the serial build first, then parallel build.
> Both
> > >> > should
> > >> > > > > happen
> > >> > > > > > > in the same folder.
> > >> > > > > > >
> > >> > > > > > > *> page 23 of amber16 manual says: *
> > >> > > > > > > *> "Do not choose any parallel options at this step! You
> > will
> > >> > need
> > >> > > to
> > >> > > > > > > install *
> > >> > > > > > > *> the serial version first; options for parallel builds
> are
> > >> > > > described
> > >> > > > > > > below *
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > > *> at Step 8. " *
> > >> > > > > > > Hai
> > >> > > > > > >
> > >> > > > > > > On Fri, Jan 13, 2017 at 3:12 PM, Ada Sedova <
> > >> > > ada.a.sedova.gmail.com>
> > >> > > > > > > wrote:
> > >> > > > > > >
> > >> > > > > > > > Thanks Scott,
> > >> > > > > > > >
> > >> > > > > > > > To answer a few of your questions:
> > >> > > > > > > >
> > >> > > > > > > > No, ORNL does not have a supported amber installation.
> We
> > >> have
> > >> > a
> > >> > > > site
> > >> > > > > > > > license for amber14 only, which is why no upgrade. If we
> > >> want
> > >> > to
> > >> > > > use
> > >> > > > > it
> > >> > > > > > > we
> > >> > > > > > > > have to download it ourselves and build.
> > >> > > > > > > >
> > >> > > > > > > > Yes, I am very familiar with the compiling procedure at
> > ORNL
> > >> > and
> > >> > > I
> > >> > > > > have
> > >> > > > > > > > submitted a help ticket, but currently no one with a
> good
> > >> > amount
> > >> > > of
> > >> > > > > > > > compiling experience here can figure out how to deal
> with
> > >> this
> > >> > > > > problem.
> > >> > > > > > > >
> > >> > > > > > > > I have the serial build in a completely different
> folder,
> > >> and I
> > >> > > ran
> > >> > > > > the
> > >> > > > > > > > parallel build complete anew, from a different login,
> > even.
> > >> > > > > > > >
> > >> > > > > > > > Yes, I do need parallel executable, as the reason we are
> > >> trying
> > >> > > to
> > >> > > > > use
> > >> > > > > > > > amber is for the DFT-MD for a larger small system.
> > >> > > > > > > >
> > >> > > > > > > > I will check the serial tests. That is strange.
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > > > Thanks again,
> > >> > > > > > > >
> > >> > > > > > > > Ada
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > > > On Fri, Jan 13, 2017 at 2:35 PM, Scott Brozell <
> > >> > > > > > sbrozell.rci.rutgers.edu
> > >> > > > > > > >
> > >> > > > > > > > wrote:
> > >> > > > > > > >
> > >> > > > > > > > > Hi,
> > >> > > > > > > > >
> > >> > > > > > > > > The most likely possibilities are probably:
> > >> > > > > > > > > 1. broken parallel tools;
> > >> > > > > > > > > 2. conflicting serial and parallel tools;
> > >> > > > > > > > > 3. residual conflicting amber files between the serial
> > and
> > >> > > > parallel
> > >> > > > > > > > builds.
> > >> > > > > > > > >
> > >> > > > > > > > > The apparent first error:
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x5a): unresolvable
> > >> > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > might be fixed with compiling options like -fpic.
> > >> > > > > > > > >
> > >> > > > > > > > > But my advice is to take a step back and tackle these
> > >> bigger
> > >> > > > > picture
> > >> > > > > > > > items:
> > >> > > > > > > > >
> > >> > > > > > > > > Doesn't ORNL have supported amber installations ?
> > >> > > > > > > > > Did you read the ORNL documentation on installing
> > >> software,
> > >> > > etc ?
> > >> > > > > > > > > Did you ask them for help ?
> > >> > > > > > > > > Do you need parallel amber executables ?
> > >> > > > > > > > > When will you upgrade to amber 16 ?
> > >> > > > > > > > > Double check your serial tests - i haven't seen all
> > >> passing
> > >> > > tests
> > >> > > > > in
> > >> > > > > > > > > amber for at least a decade.
> > >> > > > > > > > >
> > >> > > > > > > > > If you still need help from us after investigating
> those
> > >> then
> > >> > > > send
> > >> > > > > > > > > verbose and verbatim details: compiler names,
> versions,
> > >> > -show
> > >> > > > > > output,
> > >> > > > > > > > > your config.h s, the redhat-release, the complete
> build
> > >> logs,
> > >> > > > etc.
> > >> > > > > > > > >
> > >> > > > > > > > > scott
> > >> > > > > > > > >
> > >> > > > > > > > > On Fri, Jan 13, 2017 at 12:52:40PM -0500, Ada Sedova
> > >> wrote:
> > >> > > > > > > > > > I am trying to build amber14/amberTools on RHEA, an
> > OLCF
> > >> > > (ORNL)
> > >> > > > > > > > commodity
> > >> > > > > > > > > > cluster, with dual Intel® Xeon® E5-2650 CPUs, which
> > uses
> > >> > > > modules.
> > >> > > > > > > > > >
> > >> > > > > > > > > > The build was successful on the same system in
> serial,
> > >> and
> > >> > > all
> > >> > > > > > tests
> > >> > > > > > > > > passed
> > >> > > > > > > > > > after building.
> > >> > > > > > > > > >
> > >> > > > > > > > > > However, when trying to build with mpi, I am exiting
> > the
> > >> > make
> > >> > > > > > install
> > >> > > > > > > > > from
> > >> > > > > > > > > > the following folder:
> > >> > > > > > > > > >
> > >> > > > > > > > > > make[2]: Entering directory
> > >> > > > > > > > > > `/autofs/nccs-svm1_home2/adaa/
> > >> > AMBER/amber14/AmberTools/src/
> > >> > > > > > cifparse'
> > >> > > > > > > > > >
> > >> > > > > > > > > > flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c
> > >> > > > > > > > > >
> > >> > > > > > > > > > /ccs/home/adaa/AMBER/amber14/bin/yacc -v -d
> > cifparse.y
> > >> > > > > > > > > >
> > >> > > > > > > > > > make[2]: Leaving directory
> > >> > > > > > > > > > `/autofs/nccs-svm1_home2/adaa/
> > >> > AMBER/amber14/AmberTools/src/
> > >> > > > > > cifparse'
> > >> > > > > > > > > >
> > >> > > > > > > > > > make[1]: Leaving directory
> > >> > > > > > > > > > `/autofs/nccs-svm1_home2/adaa/
> > >> > AMBER/amber14/AmberTools/src'
> > >> > > > > > > > > >
> > >> > > > > > > > > > with the following error:
> > >> > > > > > > > > >
> > >> > > > > > > > > > main.o: In function `create_file_names':
> > >> > > > > > > > > >
> > >> > > > > > > > > > main.c:(.text+0x607): warning: the use of `mktemp'
> is
> > >> > > > dangerous,
> > >> > > > > > > better
> > >> > > > > > > > > use
> > >> > > > > > > > > > `mkstemp'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x5a): unresolvable
> > >> > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x6c): unresolvable
> > >> > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x73): unresolvable
> > >> > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x84): unresolvable
> > >> > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x5b1): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x5c9): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x5eb): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x60d): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x62f): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x651): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x669): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x68b): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x6ad): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x6cf): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1590): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x15f7): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1785): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x194f): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1967): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1976): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1b70): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1c41): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x1ffb): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x2002): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x2659): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x2693): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > > /usr/bin/ld: reader.o(.text+0x26ac): unresolvable
> > >> > > R_X86_64_PC32
> > >> > > > > > > > > relocation
> > >> > > > > > > > > > against symbol `cache'
> > >> > > > > > > > > >
> > >> > > > > > > > > >
> > >> > > > > > > > > > yacc:3249 terminated with signal 11 at PC=40abac
> > >> > > > SP=7fff87123600.
> > >> > > > > > > > > > Backtrace:
> > >> > > > > > > > > >
> > >> > > > > > > > > > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x40abac]
> > >> > > > > > > > > >
> > >> > > > > > > > > > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x40ce6b]
> > >> > > > > > > > > >
> > >> > > > > > > > > > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x404dfd]
> > >> > > > > > > > > >
> > >> > > > > > > > > > /lib64/libc.so.6(__libc_start_
> > >> main+0xfd)[0x7eff172bed1d]
> > >> > > > > > > > > >
> > >> > > > > > > > > > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x400ea9]
> > >> > > > > > > > > >
> > >> > > > > > > > > > make[2]: *** [cifp.tab.c] Error 1
> > >> > > > > > > > > >
> > >> > > > > > > > > > make[1]: *** [parallel] Error 2
> > >> > > > > > > > > >
> > >> > > > > > > > > > make: *** [install] Error 2
> > >> > > > > > > > >
> > >> > > > > > > > > _______________________________________________
> > >> > > > > > > > > AMBER mailing list
> > >> > > > > > > > > AMBER.ambermd.org
> > >> > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > > > > >
> > >> > > > > > > > _______________________________________________
> > >> > > > > > > > AMBER mailing list
> > >> > > > > > > > AMBER.ambermd.org
> > >> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > > > >
> > >> > > > > > > _______________________________________________
> > >> > > > > > > AMBER mailing list
> > >> > > > > > > AMBER.ambermd.org
> > >> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > > >
> > >> > > > > > _______________________________________________
> > >> > > > > > AMBER mailing list
> > >> > > > > > AMBER.ambermd.org
> > >> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > >
> > >> > > > > _______________________________________________
> > >> > > > > AMBER mailing list
> > >> > > > > AMBER.ambermd.org
> > >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > >
> > >> > > > _______________________________________________
> > >> > > > AMBER mailing list
> > >> > > > AMBER.ambermd.org
> > >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > >
> > >> > > _______________________________________________
> > >> > > AMBER mailing list
> > >> > > AMBER.ambermd.org
> > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 14 2017 - 09:30:02 PST
