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 - 03:00:03 PDT
