Hi,
Thanks for the reply Daniel. The details of the installation are follows,
$ ./configure -mpi --with-python /usr/bin/python2.7 gnu - used for
configuring Amber
Then,
$ make install - used for installation
gcc version
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --with-bugurl=
http://bugzilla.redhat.com/bugzilla
--enable-bootstrap --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-gnu-unique-object
--enable-linker-build-id --with-linker-hash-style=gnu
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto
--enable-plugin --enable-initfini-array --disable-libgcj
--with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install
--with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install
--enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64
--build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC)
MPI details
$ mpicc -show
cc -m64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-m64 -mtune=generic -fPIC -Wl,-z,noexecstack -I/usr/include/mpich-x86_64
-L/usr/lib64/mpich/lib -Wl,-rpath -Wl,/usr/lib64/mpich/lib -lmpich -lopa
-lmpl -lrt -lpthread
$ mpif90 -show
gfortran -m64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-m64 -mtune=generic -fPIC -Wl,-z,noexecstack -I/usr/include/mpich-x86_64
-I/usr/include/mpich-x86_64 -L/usr/lib64/mpich/lib -lmpichf90 -Wl,-rpath
-Wl,/usr/lib64/mpich/lib -lmpich -lopa -lmpl -lrt -lpthread
Many thanks
Anu
On Wed, Mar 16, 2016 at 4:32 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Have all updates been applied? How was Amber configured (what flags
> were used), what compilers and version, and what MPI and version are
> in use?
>
> -Dan
>
> On Wed, Mar 16, 2016 at 10:28 AM, anu chandra <anu80125.gmail.com> wrote:
> > Dear Amber users,
> >
> > While doing make test.parallel after installing AmberTools 15, I
> > experienced the following error. I have set export DO_PARALLEL='mpirun
> -np
> > 2' , before doing the test. Any help would be highly appreciated
> >
> >
> >
> *****************************************************************************************************************************************
> > make[2]: Target `test.parallel.at' not remade because of errors.
> > make[2]: Leaving directory `/usr/local/amber14/test'
> > make[2]: Entering directory `/usr/local/amber14/AmberTools/test'
> >
> > Finished test suite for AmberTools at Wed Mar 16 16:15:19 GMT 2016.
> >
> > make[2]: Leaving directory `/usr/local/amber14/AmberTools/test'
> > 370 file comparisons passed
> > 2 file comparisons failed
> > 60 tests experienced errors
> > Test log file saved as
> > /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.log
> > Test diffs file saved as
> > /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.diff
> > make[1]: Leaving directory `/usr/local/amber14/AmberTools/test'
> > ==============================================================
> > /usr/local/amber14/src/Makefile not found.
> > This is expected if you have not installed Amber14.
> > ==============================================================
> >
> >
> ***************************************************************************************************************************************
> >
> >
> > Part of the
> > /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.log is shown
> > below,
> >
> >
> >
> >
> **************************************************************************************************************************************
> > export TESTsander=/usr/local/amber14/bin/sander.MPI; cd jar_multi &&
> > ./Run.jarz
> >
> > Running multisander version of sander Amber14
> > Total processors = 2
> > Number of groups = 2
> >
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> > Backtrace for this error:
> > #0 0x7F482577D467
> > #1 0x7F482577DAAE
> > #2 0x7F4824C8466F
> > #3 0x7F482583ABE8
> > #4 0x5C1C51 in amopen_ at amopen.F90:90 (discriminator 1)
> > #5 0x508FD7 in mdread1_ at mdread1.F90:182
> > #6 0x4D6159 in sander_ at sander.F90:326
> > #7 0x4D4E12 in multisander at multisander.F90:436
> >
> >
> ===================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = EXIT CODE: 139
> > = CLEANING UP REMAINING PROCESSES
> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >
> ===================================================================================
> > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
> > (signal 11)
> > This typically refers to a problem with your application.
> > Please see the FAQ page for debugging suggestions
> > ./Run.jarz: Program error
> > make[2]: [test.sander.BASIC.MPI] Error 1 (ignored)
> > export TESTsander=/usr/local/amber14/bin/sander.MPI; cd ti_eth2meth_gas
> &&
> > ./Run.test1
> >
> > Running multisander version of sander Amber14
> > Total processors = 2
> > Number of groups = 2
> >
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> > Backtrace for this error:
> > #0 0x7FBD4B1CB467
> > #1 0x7FBD4B1CBAAE
> > #2 0x7FBD4A6D266F
> > #3 0x7FBD4B288BE8
> > #4 0x5C1C51 in amopen_ at amopen.F90:90 (discriminator 1)
> > #5 0x508FD7 in mdread1_ at mdread1.F90:182
> > #6 0x4D6159 in sander_ at sander.F90:326
> > #7 0x4D4E12 in multisander at multisander.F90:436
> >
> >
> ===================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> >
> >
> >
> **************************************************************************************************************************************************
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 17 2016 - 06:30:03 PDT
