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
Received on Sat Jan 14 2017 - 09:30:02 PST
