Hi there,
My first posting/experience with Palabos so I may be missing something very obvious here.
I compiled without any problem the example in
~/palabos-v0.7r0/examples/showCases/cavity2d
and it runs fine.
The python interface however is giving me some troubles: any help will be highly appreciated. Many thanks in advance
Sincerely
Andrea
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ make
cd compilePalabos; make
make[1]: Entering directory /home/shabela/palabos-v0.7r0/pythonic/src/compilePalabos' python /home/shabela/palabos-v0.7r0/pythonic/src/compilePalabos/../../..//scons/scons.py -f /home/shabela/palabos-v0.7r0/pythonic/src/compilePalabos/../../..//SConstruct palabosRoot=/home/shabela/palabos-v0.7r0/pythonic/src/compilePalabos/../../../ projectFiles="dummyMain.cpp" precompiled=false optimize=true debug=false profile=false MPIparallel=true SMPparallel=false usePOSIX=true useCVMLCPP=false serialCXX=g++ parallelCXX=mpicxx dynamicLibrary=true compileFlags="-Wall" linkFlags="" optimFlags="-O3" debugFlags="-g" profileFlags="-pg" libraryPaths="" includePaths="" libraries="" scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons:.’ is up to date.
scons: done building targets.
make[1]: Leaving directory /home/shabela/palabos-v0.7r0/pythonic/src/compilePalabos' bash ./preprocess ~/palabos-v0.7r0/pythonic/src/swig ~/palabos-v0.7r0/pythonic/src Swig-file preparation for module core sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' Swig-file specialization for module int_block sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' Swig-file specialization for module double_block sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' Swig-file specialization for module float_block sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' Swig-file specialization for module double_d2q9 sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' Swig-file specialization for module float_d2q9 sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' Swig-file specialization for module double_d3q19 sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' Swig-file specialization for module float_d3q19 sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 42: unknown option tos’
sed: -e expression #1, char 40: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to s' sed: -e expression #1, char 40: unknown option tos’
sed: -e expression #1, char 42: unknown option to `s’
~/palabos-v0.7r0/pythonic/src
python /home/shabela/palabos-v0.7r0/scons/scons.py -f /home/shabela/palabos-v0.7r0/pythonic/src//SConstruct palabosRoot=/home/shabela/palabos-v0.7r0 pypalRoot=/home/shabela/palabos-v0.7r0/pythonic/src/ optimize=true debug=false profile=false MPIparallel=true serialCXX=g++ parallelCXX=mpicxx compileFlags="-Wall" optimFlags="-O3" debugFlags="-g" profileFlags="-pg" includePaths="" linkFlags=""
scons: Reading SConscript files …
scons: done reading SConscript files.
scons: Building targets …
swig -o swig/core/pre_processed/core_wrap.cc -classic -python -c++ swig/core/pre_processed/core.i
No module name specified using %module or -module.
scons: *** [swig/core/pre_processed/core_wrap.cc] Error 1
scons: building terminated because of errors.
make: *** [compilation] Error 2
I think I have installed all the dependencies that are required at :
http://www.lbmethod.org/palabos/documentation.userguide/pythonic.html?highlight=python
in particular:
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ echo $PALABOS_ROOT
/home/shabela/palabos-v0.7r0
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic$ sudo apt-get install swig
Reading package lists… Done
Building dependency tree
Reading state information… Done
swig is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic$ sudo easy_install mpi4py
Searching for mpi4py
Best match: mpi4py 1.2.1
Processing mpi4py-1.2.1-py2.6-linux-i686.egg
mpi4py 1.2.1 is already the active version in easy-install.pth
Using /usr/local/lib/python2.6/dist-packages/mpi4py-1.2.1-py2.6-linux-i686.egg
Processing dependencies for mpi4py
Finished processing dependencies for mpi4py
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ sudo apt-get install mpi-default-dev
Reading package lists… Done
Building dependency tree
Reading state information… Done
mpi-default-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ sudo apt-get install mpi-default-bin
Reading package lists… Done
Building dependency tree
Reading state information… Done
mpi-default-bin is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ sudo apt-get install python
Reading package lists… Done
Building dependency tree
Reading state information… Done
python is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ python
Python 2.6.5 (r265:79063, Apr 16 2010, 13:09:56)
[GCC 4.4.3] on linux2
Type “help”, “copyright”, “credits” or “license” for more information.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ sudo apt-get install python-dev
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ sudo apt-get install python-setuptools
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-setuptools is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic$ sudo apt-get install python-numpy
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-numpy is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic$ sudo apt-get install python-scipy
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-scipy is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic$ sudo apt-get install python-matplotlib
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-matplotlib is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ sudo apt-get install mayavi2
Reading package lists… Done
Building dependency tree
Reading state information… Done
mayavi2 is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ mayavi2 -V
Mayavi 3.3.0
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ g++ -v
Using built-in specs.
Target: i486-linux-gnu
Configured with: …/src/configure -v --with-pkgversion=‘Ubuntu 4.4.3-4ubuntu5’ --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-plugin --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=i486-linux-gnu --host=i486-linux-gnu --target=i486-linux-gnu
Thread model: posix
gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ gcc -v
Using built-in specs.
Target: i486-linux-gnu
Configured with: …/src/configure -v --with-pkgversion=‘Ubuntu 4.4.3-4ubuntu5’ --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-plugin --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=i486-linux-gnu --host=i486-linux-gnu --target=i486-linux-gnu
Thread model: posix
gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
SPECIFIC INFORMATION ON MY MACHINE
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ uname -a
Linux shabela-laptop 2.6.32-24-generic #38-Ubuntu SMP Mon Jul 5 09:22:14 UTC 2010 i686 GNU/Linux
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ cat /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 13
model name : Intel® Pentium® M processor 1.20GHz
stepping : 8
cpu MHz : 600.000
cache size : 2048 KB
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 2
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov clflush dts acpi mmx fxsr sse sse2 ss tm pbe nx up bts est tm2
bogomips : 1196.98
clflush size : 64
cache_alignment : 64
address sizes : 32 bits physical, 32 bits virtual
power management:
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ cat /proc/meminfo
MemTotal: 1534524 kB
MemFree: 111312 kB
Buffers: 113800 kB
Cached: 928272 kB
SwapCached: 2732 kB
Active: 622120 kB
Inactive: 722884 kB
Active(anon): 136840 kB
Inactive(anon): 303028 kB
Active(file): 485280 kB
Inactive(file): 419856 kB
Unevictable: 0 kB
Mlocked: 0 kB
HighTotal: 653896 kB
HighFree: 12524 kB
LowTotal: 880628 kB
LowFree: 98788 kB
SwapTotal: 2441840 kB
SwapFree: 2434436 kB
Dirty: 56 kB
Writeback: 0 kB
AnonPages: 300976 kB
Mapped: 117068 kB
Shmem: 136936 kB
Slab: 48436 kB
SReclaimable: 32752 kB
SUnreclaim: 15684 kB
KernelStack: 2136 kB
PageTables: 7392 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 3209100 kB
Committed_AS: 1067064 kB
VmallocTotal: 122880 kB
VmallocUsed: 24196 kB
VmallocChunk: 65416 kB
HardwareCorrupted: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 4096 kB
DirectMap4k: 24568 kB
DirectMap4M: 884736 kB
shabela@shabela-laptop:~/palabos-v0.7r0/pythonic/src$ lspci
00:00.0 Host bridge: Intel Corporation Mobile 915GM/PM/GMS/910GML Express Processor to DRAM Controller (rev 03)
00:02.0 VGA compatible controller: Intel Corporation Mobile 915GM/GMS/910GML Express Graphics Controller (rev 03)
00:02.1 Display controller: Intel Corporation Mobile 915GM/GMS/910GML Express Graphics Controller (rev 03)
00:1b.0 Audio device: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) High Definition Audio Controller (rev 03)
00:1d.0 USB Controller: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) USB UHCI #1 (rev 03)
00:1d.1 USB Controller: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) USB UHCI #2 (rev 03)
00:1d.2 USB Controller: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) USB UHCI #3 (rev 03)
00:1d.3 USB Controller: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) USB UHCI #4 (rev 03)
00:1d.7 USB Controller: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) USB2 EHCI Controller (rev 03)
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev d3)
00:1f.0 ISA bridge: Intel Corporation 82801FBM (ICH6M) LPC Interface Bridge (rev 03)
00:1f.1 IDE interface: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) IDE Controller (rev 03)
00:1f.3 SMBus: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) SMBus Controller (rev 03)
06:05.0 CardBus bridge: Texas Instruments PCIxx21/x515 Cardbus Controller
06:05.2 FireWire (IEEE 1394): Texas Instruments OHCI Compliant IEEE 1394 Host Controller
06:05.3 Mass storage controller: Texas Instruments PCIxx21 Integrated FlashMedia Controller
06:08.0 Ethernet controller: Intel Corporation 82562EM/EX/GX - PRO/100 VM (LOM) Ethernet Controller Mobile (rev 03)
06:0b.0 Network controller: Intel Corporation PRO/Wireless 2200BG [Calexico2] Network Connection (rev 05)