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
> >
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Received on Fri Jan 13 2017 - 12:30:03 PST
