Sorry everybody for the stupid post,
I messed up the deffinition of DO_PARALLEL ...(shoudl be "mpirun -np 4"
and not "nab")
Everything is fine now....
Vlad
On 07/23/2010 11:52 AM, Vlad Cojocaru wrote:
> Dear all,
>
> I compiled AmberTools 1.4 serial ... All tests passed. Then I compiled
> the parallel versions of nab and ptraj .. Aparently the compilation went
> well (no errors upon make)..
>
> However all tests fail :
> After setting "export DO_PARALLEL=$AMBERHOME/bin/nab" I run the tests
> with "make test.parallel"
> The errors are below ...
>
> Is anybody aware of these failures ?
>
> My architecture is: openSUSE x86_64, gcc 4.5.0, openmpi 1.4.2, 8 cores
> per node.
>
> Best wishes
> Vlad
>
> Here is the output of "ldd nab" .. It seems linking worked well
> linux-vdso.so.1 => (0x00007fff80dff000)
> libmpi.so.0 => /usr/local/apps/openmpi/1.4.2/lib/libmpi.so.0
> (0x00007fce077be000)
> libopen-rte.so.0 =>
> /usr/local/apps/openmpi/1.4.2/lib/libopen-rte.so.0 (0x00007fce0756e000)
> libopen-pal.so.0 =>
> /usr/local/apps/openmpi/1.4.2/lib/libopen-pal.so.0 (0x00007fce07315000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00007fce07111000)
> libnsl.so.1 => /lib64/libnsl.so.1 (0x00007fce06ef9000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00007fce06cf6000)
> libm.so.6 => /lib64/libm.so.6 (0x00007fce06a9f000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fce06882000)
> libc.so.6 => /lib64/libc.so.6 (0x00007fce06522000)
> /lib64/ld-linux-x86-64.so.2 (0x00007fce07a6c000)
>
>
>
>
>
> -------------------- ERRORS -------------------
>
> ./test_at_parallel.sh
> make[1]: Entering directory `/usr/local/build-apps/amber/11/AmberTools/test'
> (find antechamber -name '*.out' -o -name '*.log' -o -name '*.lib' -o \
> -name "*.dif" | \
> while read dif ;\
> do \
> rm -f $dif ;\
> done ;\
> )
> (cd leap && /bin/rm -f *.log *.out *.lib *.top )
> (cd ptraj_rmsa && /bin/rm -f *.dif )
> (cd ptraj_matrix && /bin/rm -f *.dif )
> (cd ptraj_rms && /bin/rm -f *.dif )
> (cd ptraj_les && /bin/rm -f *.dif )
> (find sleap -name '*.out' -o -name '*.log' -o -name '*.lib' -o \
> -name "*.dif" | \
> while read dif ;\
> do \
> rm -f $dif ;\
> done ;\
> )
> (find sqm -name '*.out' -o -name '*.dif' | \
> while read dif ;\
> do \
> rm -f $dif ;\
> done ;\
> )
> /bin/rm -f TEST_FAILURES.diff
> cd nab && make -k test
> make[2]: Entering directory
> `/usr/local/build-apps/amber/11/AmberTools/test/nab'
> Running test to do simple minimization
> (this tests the molecular mechanics interface)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.sff: Program error
> make[2]: *** [sff_test] Error 1
> Running test to do simple minimization with shake
> (this tests the molecular mechanics interface)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.shake: Program error
> make[2]: *** [rattle_min_test] Error 1
> Running test of fibre-diffraction module
>
> ./fd: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./fd: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./fd:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./fd: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./fd: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./fd(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.fd: Program error
> make[2]: *** [fd_test] Error 1
> Running test to do simple minimization
> (this tests the generalized Born implementation)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.gb: Program error
> make[2]: *** [gb_test] Error 1
> Running test to do simple minimization
> (this tests the generalized Born implementation)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.xfin: Program error
> make[2]: *** [xfin_test] Error 1
> Running test to do simple minimization
> (this tests the LCPO surface area)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.gbsa: Program error
> make[2]: *** [gbsa_test] Error 1
> Running test to do simple minimization
> (this tests the ao generalized Born implementation)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.gb2: Program error
> make[2]: *** [gb2_test] Error 1
> Running test to do molecular dynamics with rattle
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.rattle_md: Program error
> make[2]: *** [rattle_md_test] Error 1
> Running test to compute NAB energy of 3dfr minus waters.
>
> ./dhfrndpmtx: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./dhfrndpmtx: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./dhfrndpmtx:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./dhfrndpmtx: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./dhfrndpmtx: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./dhfrndpmtx(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.dhfrndpmtx: Program error
> make[2]: *** [dhfrndpmtx_test] Error 1
> Running test to compute GB Newton-Raphson and normal modes:
>
> ./asp: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./asp: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./asp:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./asp: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./asp: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./asp(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.asp: Program error
> make[2]: *** [asp_test] Error 1
> Running test to compute non-GB Newton-Raphson and normal modes:
>
> ./aspnb: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./aspnb: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./aspnb:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./aspnb: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./aspnb: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./aspnb(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.aspnb: Program error
> make[2]: *** [aspnb_test] Error 1
> Running test to create Amber force-field description
>
> ./prm: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./prm: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./prm:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./prm: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./prm: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./prm(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.prm: Program error
> make[2]: *** [prm_test] Error 1
> Running test to do simple xmin minimization
>
> ./txmin: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./txmin: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./txmin:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./txmin: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./txmin: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./txmin(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.xmin: Program error
> make[2]: *** [xmin_test] Error 1
> Running test to do simple lmod optimization
>
> ./tlmod: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./tlmod: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./tlmod:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./tlmod: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./tlmod: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./tlmod(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> diffing tlmod.out.check with tlmod.out
> PASSED
> ==============================================================
> Running test to compute GB normal modes using DSYEVD:
>
> ./asp_nm1: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./asp_nm1: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./asp_nm1:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./asp_nm1: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./asp_nm1: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./asp_nm1(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.nmode1: Program error
> make[2]: *** [nmode1_test] Error 1
> Running test to compute GB normal modes using DSAUPD:
>
> ./asp_nm2: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./asp_nm2: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./asp_nm2:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./asp_nm2: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./asp_nm2: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./asp_nm2(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.nmode2: Program error
> make[2]: *** [nmode2_test] Error 1
> Running test to compute Langevin modes:
>
> ./asp_nm3: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./asp_nm3: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./asp_nm3:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./asp_nm3: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./asp_nm3: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./asp_nm3(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.nmode3: Program error
> make[2]: *** [nmode3_test] Error 1
> Running test of the isotropic periodic sum technique
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.ips: Program error
> make[2]: *** [ips_test] Error 1
> Running test to do simple minimization (libpbsa)
> (this tests the PBSA implementation)
>
> ./sff: In function `_start':
> /usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> multiple definition of `_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:/usr/src/packages/BUILD/glibc-2.11.2/csu/../sysdeps/x86_64/elf/start.S:65:
> first defined here
> ./sff: In function `_fini':
> (.fini+0x0): multiple definition of `_fini'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.fini+0x0):
> first defined here
> ./sff:(.rodata+0x0): multiple definition of `_IO_stdin_used'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.rodata.cst4+0x0):
> first defined here
> ./sff: In function `__data_start':
> (.data+0x0): multiple definition of `__data_start'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crt1.o:(.data+0x0):
> first defined here
> ./sff: In function `_init':
> (.init+0x0): multiple definition of `_init'
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o:initfini.c:(.init+0x0):
> first defined here
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> warning: Cannot create .eh_frame_hdr section, --eh-frame-hdr ignored.
> /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld:
> error in ./sff(.eh_frame); no .eh_frame_hdr table will be created.
> collect2: ld returned 1 exit status
> cc failed!
> ./Run.pbsa: Program error
> make[2]: *** [pbsa_test] Error 1
> make[2]: Target `test' not remade because of errors.
> make[2]: Leaving directory
> `/usr/local/build-apps/amber/11/AmberTools/test/nab'
> make[1]: *** [test.nab] Error 2
> cd ptraj_comprehensive && ./Run.comprehensive yes
>
> ptraj: Test multiple ptraj actions.
> Trying to run test with threads.
> The parallel version of this test case requires either 2 or 4 threads.
> Not running test, exiting.....
>
>
> Finished test suite for parallel AmberTools (ptraj) at Fri Jul 23
> 11:24:40 CEST 2010.
>
>
> Finished test suite for AmberTools at Fri Jul 23 11:24:40 CEST 2010.
>
> make[1]: Target `test.parallel2' not remade because of errors.
> make[1]: Leaving directory `/usr/local/build-apps/amber/11/AmberTools/test'
> 1 file comparison passed
> 0 file comparisons failed
> 58 tests experienced errors
> Test log file saved as logs/test_at_parallel/2010-07-23_11-24-36.log
> No test diffs to save!
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Jul 23 2010 - 03:30:03 PDT
