I will try, burt honestly, looking at the error, it seems that this is a
result of a discrepancy between my redhat version of the yacc parser's
syntax and the way it is called in the cifparse script.
On Sat, Jan 14, 2017 at 12:09 PM, Nhai <nhai.qn.gmail.com> wrote:
> Do you have tar file for your amber14? If yes,
> use it for super fresh install.
>
> Let us if that helps or not. Cheers
>
> Hai
>
> > On Jan 14, 2017, at 12:01 PM, Ada Sedova <ada.a.sedova.gmail.com> wrote:
> >
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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Received on Sat Jan 14 2017 - 09:30:03 PST
