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
> >
> _______________________________________________
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>
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Received on Fri Jan 13 2017 - 21:30:02 PST
