fishdude
24-Nov-2011, 06:39
Hi,
I'm having trouble building libatlas from the src.rpm of the Education repo for openSUSE 12.1.
I use the following command:
rpmbuild --rebuild libatlas-3.9.35-33.4.src.rpm
The build finishes producing the desired rpm's, but these lack the threaded libraries:
libptlapack.a
libptcblas.a
libptf77blas.a
which prevents the utilization of multiple cores.
Digging around in the build output the following was discovered:
<snip>
make[4]: Entering directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads'
rm res/probe.out
rm: cannot remove `res/probe.out': No such file or directory
make[4]: [IRun_aff] Error 1 (ignored)
./xprobe_aff -v 1 -o /usr/src/packages/BUILD/ATLAS/x86_64_base/include/atlas_taffinity.h
*** glibc detected *** ./xprobe_aff: free(): invalid pointer: 0x0000000000607010 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x74c06)[0x7ff01704ac06]
./xprobe_aff[0x401a01]
/lib64/libc.so.6(__libc_start_main+0xed)[0x7ff016ff723d]
./xprobe_aff[0x400d59]
======= Memory map: ========
00400000-00405000 r-xp 00000000 08:01 900364 /usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads/xprobe_aff
00605000-00606000 r--p 00005000 08:01 900364 /usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads/xprobe_aff
00606000-00607000 rw-p 00006000 08:01 900364 /usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads/xprobe_aff
00607000-00628000 rw-p 00000000 00:00 0 [heap]
7ff016dc0000-7ff016dd5000 r-xp 00000000 08:01 293547 /lib64/libgcc_s.so.1
7ff016dd5000-7ff016fd4000 ---p 00015000 08:01 293547 /lib64/libgcc_s.so.1
7ff016fd4000-7ff016fd5000 r--p 00014000 08:01 293547 /lib64/libgcc_s.so.1
7ff016fd5000-7ff016fd6000 rw-p 00015000 08:01 293547 /lib64/libgcc_s.so.1
7ff016fd6000-7ff01715b000 r-xp 00000000 08:01 293244 /lib64/libc-2.14.1.so
7ff01715b000-7ff01735b000 ---p 00185000 08:01 293244 /lib64/libc-2.14.1.so
7ff01735b000-7ff01735f000 r--p 00185000 08:01 293244 /lib64/libc-2.14.1.so
7ff01735f000-7ff017360000 rw-p 00189000 08:01 293244 /lib64/libc-2.14.1.so
7ff017360000-7ff017365000 rw-p 00000000 00:00 0
7ff017365000-7ff0173bb000 r-xp 00000000 08:01 293259 /lib64/libm-2.14.1.so
7ff0173bb000-7ff0175ba000 ---p 00056000 08:01 293259 /lib64/libm-2.14.1.so
7ff0175ba000-7ff0175bb000 r--p 00055000 08:01 293259 /lib64/libm-2.14.1.so
7ff0175bb000-7ff0175bc000 rw-p 00056000 08:01 293259 /lib64/libm-2.14.1.so
7ff0175bc000-7ff0175d4000 r-xp 00000000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0175d4000-7ff0177d3000 ---p 00018000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0177d3000-7ff0177d4000 r--p 00017000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0177d4000-7ff0177d5000 rw-p 00018000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0177d5000-7ff0177d9000 rw-p 00000000 00:00 0
7ff0177d9000-7ff0177f9000 r-xp 00000000 08:01 293225 /lib64/ld-2.14.1.so
7ff0179cd000-7ff0179d0000 rw-p 00000000 00:00 0
7ff0179f5000-7ff0179f9000 rw-p 00000000 00:00 0
7ff0179f9000-7ff0179fa000 r--p 00020000 08:01 293225 /lib64/ld-2.14.1.so
7ff0179fa000-7ff0179fb000 rw-p 00021000 08:01 293225 /lib64/ld-2.14.1.so
7ff0179fb000-7ff0179fc000 rw-p 00000000 00:00 0
7fff2d7b7000-7fff2d7d8000 rw-p 00000000 00:00 0 [stack]
7fff2d7ff000-7fff2d800000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
SETAFFNP: DETECTED!
FINDING LARGEST POWER OF 2 ID THAT CAN BE USED IN AFFINITY:
ID=1 works.
ID=2 works.
ID=4 FAILS.
ID=8 FAILS.
ID=16 FAILS.
ID=32 FAILS.
ID=64 FAILS.
ID=128 FAILS.
LARGEST SUCCESSFUL POWER OF 2 = 2
FINDING ALL VALID IDs BETWEEN 0 AND 3:
ID=1 works.
ID=2 works.
ID=3 works.
AFFINITY TYPE= 'SETAFFNP'
All IDs between [0, 3] are valid
make[4]: *** [IRun_aff] Aborted
make[4]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads'
make[3]: *** [/usr/src/packages/BUILD/ATLAS/x86_64_base/include/atlas_pthreads.h] Error 2
make[3]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/src/auxil'
make[2]: *** [IBuildPtlibs0] Error 2
make[2]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/bin'
DONE STAGE 5-1-0 at 12:10
<snip/>
This seems to prevent the build of the pt-libs.
<snip>
make[7]: Entering directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
gcc -m64 -fPIC -shared -o libtatlas.so -Wl,"rpath-link /usr/src/packages/BUILDROOT/libatlas3-3.9.35-33.4.x86_64/usr/lib64/atlas" \
-Wl,--whole-archive libptlapack.a libptf77blas.a libptcblas.a libatlas.a -Wl,--no-whole-archive -L/usr/lib64/gcc/x86_64-suse-linux/4.6 -lgfortran -lc -lpthread -lm -lgcc
gcc: error: libptlapack.a: No such file or directory
gcc: error: libptf77blas.a: No such file or directory
gcc: error: libptcblas.a: No such file or directory
make[7]: *** [GCCTRY] Error 1
make[7]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[7]: Entering directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
mkdir static_libs ; pushd static_libs && ar x ../libptlapack.a; ar x ../libptf77blas.a; ar x ../libptcblas.a; ar x ../libatlas.a; popd ; \
gcc -melf_x86_64 -shared -Wl,-soname=libtatlas.so.3 \
-o libtatlas.so.3.0 static_libs/*.o -lc -L/usr/lib64/gcc/x86_64-suse-linux/4.6 -lgfortran -lc -lpthread -lm -lgcc ; \
rm -rf static_libs
/usr/src/packages/BUILD/ATLAS/x86_64_base/lib/static_libs /usr/src/packages/BUILD/ATLAS/x86_64_base/lib
ar: ../libptlapack.a: No such file or directory
ar: ../libptf77blas.a: No such file or directory
ar: ../libptcblas.a: No such file or directory
/usr/src/packages/BUILD/ATLAS/x86_64_base/lib
make[7]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
libtatlas.so built wt ld and all sys libs
make[6]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[5]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[4]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[3]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base'
make[2]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/bin'
DONE STAGE 5-2-0 at 12:10
<snip/>
Building on 11.4 shows no such problems.
I even took the src.rpm for 11.4 which was building fine and tried to rebuild this on 12.1.
Results where the same.
Any help is appreciated, thanks.
I'm having trouble building libatlas from the src.rpm of the Education repo for openSUSE 12.1.
I use the following command:
rpmbuild --rebuild libatlas-3.9.35-33.4.src.rpm
The build finishes producing the desired rpm's, but these lack the threaded libraries:
libptlapack.a
libptcblas.a
libptf77blas.a
which prevents the utilization of multiple cores.
Digging around in the build output the following was discovered:
<snip>
make[4]: Entering directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads'
rm res/probe.out
rm: cannot remove `res/probe.out': No such file or directory
make[4]: [IRun_aff] Error 1 (ignored)
./xprobe_aff -v 1 -o /usr/src/packages/BUILD/ATLAS/x86_64_base/include/atlas_taffinity.h
*** glibc detected *** ./xprobe_aff: free(): invalid pointer: 0x0000000000607010 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x74c06)[0x7ff01704ac06]
./xprobe_aff[0x401a01]
/lib64/libc.so.6(__libc_start_main+0xed)[0x7ff016ff723d]
./xprobe_aff[0x400d59]
======= Memory map: ========
00400000-00405000 r-xp 00000000 08:01 900364 /usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads/xprobe_aff
00605000-00606000 r--p 00005000 08:01 900364 /usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads/xprobe_aff
00606000-00607000 rw-p 00006000 08:01 900364 /usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads/xprobe_aff
00607000-00628000 rw-p 00000000 00:00 0 [heap]
7ff016dc0000-7ff016dd5000 r-xp 00000000 08:01 293547 /lib64/libgcc_s.so.1
7ff016dd5000-7ff016fd4000 ---p 00015000 08:01 293547 /lib64/libgcc_s.so.1
7ff016fd4000-7ff016fd5000 r--p 00014000 08:01 293547 /lib64/libgcc_s.so.1
7ff016fd5000-7ff016fd6000 rw-p 00015000 08:01 293547 /lib64/libgcc_s.so.1
7ff016fd6000-7ff01715b000 r-xp 00000000 08:01 293244 /lib64/libc-2.14.1.so
7ff01715b000-7ff01735b000 ---p 00185000 08:01 293244 /lib64/libc-2.14.1.so
7ff01735b000-7ff01735f000 r--p 00185000 08:01 293244 /lib64/libc-2.14.1.so
7ff01735f000-7ff017360000 rw-p 00189000 08:01 293244 /lib64/libc-2.14.1.so
7ff017360000-7ff017365000 rw-p 00000000 00:00 0
7ff017365000-7ff0173bb000 r-xp 00000000 08:01 293259 /lib64/libm-2.14.1.so
7ff0173bb000-7ff0175ba000 ---p 00056000 08:01 293259 /lib64/libm-2.14.1.so
7ff0175ba000-7ff0175bb000 r--p 00055000 08:01 293259 /lib64/libm-2.14.1.so
7ff0175bb000-7ff0175bc000 rw-p 00056000 08:01 293259 /lib64/libm-2.14.1.so
7ff0175bc000-7ff0175d4000 r-xp 00000000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0175d4000-7ff0177d3000 ---p 00018000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0177d3000-7ff0177d4000 r--p 00017000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0177d4000-7ff0177d5000 rw-p 00018000 08:01 293315 /lib64/libpthread-2.14.1.so
7ff0177d5000-7ff0177d9000 rw-p 00000000 00:00 0
7ff0177d9000-7ff0177f9000 r-xp 00000000 08:01 293225 /lib64/ld-2.14.1.so
7ff0179cd000-7ff0179d0000 rw-p 00000000 00:00 0
7ff0179f5000-7ff0179f9000 rw-p 00000000 00:00 0
7ff0179f9000-7ff0179fa000 r--p 00020000 08:01 293225 /lib64/ld-2.14.1.so
7ff0179fa000-7ff0179fb000 rw-p 00021000 08:01 293225 /lib64/ld-2.14.1.so
7ff0179fb000-7ff0179fc000 rw-p 00000000 00:00 0
7fff2d7b7000-7fff2d7d8000 rw-p 00000000 00:00 0 [stack]
7fff2d7ff000-7fff2d800000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
SETAFFNP: DETECTED!
FINDING LARGEST POWER OF 2 ID THAT CAN BE USED IN AFFINITY:
ID=1 works.
ID=2 works.
ID=4 FAILS.
ID=8 FAILS.
ID=16 FAILS.
ID=32 FAILS.
ID=64 FAILS.
ID=128 FAILS.
LARGEST SUCCESSFUL POWER OF 2 = 2
FINDING ALL VALID IDs BETWEEN 0 AND 3:
ID=1 works.
ID=2 works.
ID=3 works.
AFFINITY TYPE= 'SETAFFNP'
All IDs between [0, 3] are valid
make[4]: *** [IRun_aff] Aborted
make[4]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/tune/threads'
make[3]: *** [/usr/src/packages/BUILD/ATLAS/x86_64_base/include/atlas_pthreads.h] Error 2
make[3]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/src/auxil'
make[2]: *** [IBuildPtlibs0] Error 2
make[2]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/bin'
DONE STAGE 5-1-0 at 12:10
<snip/>
This seems to prevent the build of the pt-libs.
<snip>
make[7]: Entering directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
gcc -m64 -fPIC -shared -o libtatlas.so -Wl,"rpath-link /usr/src/packages/BUILDROOT/libatlas3-3.9.35-33.4.x86_64/usr/lib64/atlas" \
-Wl,--whole-archive libptlapack.a libptf77blas.a libptcblas.a libatlas.a -Wl,--no-whole-archive -L/usr/lib64/gcc/x86_64-suse-linux/4.6 -lgfortran -lc -lpthread -lm -lgcc
gcc: error: libptlapack.a: No such file or directory
gcc: error: libptf77blas.a: No such file or directory
gcc: error: libptcblas.a: No such file or directory
make[7]: *** [GCCTRY] Error 1
make[7]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[7]: Entering directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
mkdir static_libs ; pushd static_libs && ar x ../libptlapack.a; ar x ../libptf77blas.a; ar x ../libptcblas.a; ar x ../libatlas.a; popd ; \
gcc -melf_x86_64 -shared -Wl,-soname=libtatlas.so.3 \
-o libtatlas.so.3.0 static_libs/*.o -lc -L/usr/lib64/gcc/x86_64-suse-linux/4.6 -lgfortran -lc -lpthread -lm -lgcc ; \
rm -rf static_libs
/usr/src/packages/BUILD/ATLAS/x86_64_base/lib/static_libs /usr/src/packages/BUILD/ATLAS/x86_64_base/lib
ar: ../libptlapack.a: No such file or directory
ar: ../libptf77blas.a: No such file or directory
ar: ../libptcblas.a: No such file or directory
/usr/src/packages/BUILD/ATLAS/x86_64_base/lib
make[7]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
libtatlas.so built wt ld and all sys libs
make[6]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[5]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[4]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/lib'
make[3]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base'
make[2]: Leaving directory `/usr/src/packages/BUILD/ATLAS/x86_64_base/bin'
DONE STAGE 5-2-0 at 12:10
<snip/>
Building on 11.4 shows no such problems.
I even took the src.rpm for 11.4 which was building fine and tried to rebuild this on 12.1.
Results where the same.
Any help is appreciated, thanks.