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
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Received on Fri Jan 13 2017 - 12:00:02 PST
