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[OpenFOAM.org] OpenFOAM build on Intel Xeon Phi |
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May 29, 2013, 18:40 |
OpenFOAM build on Intel Xeon Phi
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#1 |
New Member
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Hi, foamers.
Today, I'd like to report my experience on building an OpenFOAM native MPI solver on Xeon Phi (Intel's co-processor and accelalator parts of the next world fastest supercomputer.) Building OpenFOAM for Xeon Phi is bit tricky, but not difficult. 1. Make Zlib and Flex for Xeon Phi 2. Set OpenFOAM bashrc/setting.sh to linux64Icc and INTEL MPI 3. Make wmake only 4. Add -mmic to wmake/rules/linux64ICC/{c, c++} 5. Compile OpenFOAM libraries. If compilation fails, add Zlib/Flex path to Make/options 6. Compile solver applicaitions. You'll get many undefined function errors. Then use mpiicpc compiler (not icpc) and add -Wl,rpath-link flag for appropirate library's path by manual. Finally, I got icoFoam for Xeon Phi. Perhaps there is an easier and canonical way. I use Xeon Phi 5110P model. It has phisically 60 cores appeared as virtually 240 cores by Intel's Hyperthreading technology and 8GB GDDR5 memory. The benchmark case is 3 dimensional caivty flow (modified from icoFoam's tutorial case) and I varied the MPI processes from 30 to 240. Benchmark conditions: Modified icoFoam tutorial cavity case (OpenFOAM-2.2.0) 3D cavity problem, deltaT = 1e-4, 50 time steps Problem size: SMALL: (90x90x90) LEFT AXIS , LARGE: (175,175,175) RIGHT AXIS CXXFLAGS = -mmic -O2 -no-prec-div Domain decomposed by scotch This is the result: http://www.cfd-online.com/Forums/att...1&d=1369863305 You can compare figures with your own results. Running an OpenFOAM solver on Xeon Phi without any source code modification is possible. But if you want the performance coressponding to the price, you should optimize your code. Cheers. -- asaijo Last edited by asaijo; May 31, 2013 at 14:33. Reason: fix typos and add sentences |
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May 30, 2013, 00:04 |
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#2 |
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luchen
Join Date: Jul 2011
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hello,asaijo, I am intrested in your computer, can you tell me how do you set the configuration for the computer? is it the same as in normal computer? have you conduct some simulations?what about the performace?
Besides, did you use NVIDIA Tesla K20 Architecture with CUDA-Option for simulation? did you compare the performance of NVIDIA Tesla K20 Architecture with CUDA-Option or the Intel Xeon Phi Technology? thanks |
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May 31, 2013, 14:49 |
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#3 |
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Hi, luchen2408.
The machine is normal and standard server, bought from local vendor. Basic configurations has been set by the vendor. But I had to install a compiler, libraries and do extra tweaks for use. I haven't used the K20X yet. Regards. |
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June 2, 2013, 09:54 |
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#4 |
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luchen
Join Date: Jul 2011
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hello,asaijo,thanks for your reply, can I take the Xeon Phi computer as a normal computer with many cores? and can I intall the software openfoam like an normal computer and use the same command in a normal multi-cores computer? thanks
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June 3, 2013, 00:47 |
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#5 |
New Member
Qiao
Join Date: May 2013
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hi, asaijo
I have got an Intel Xeon Phi card and want to build an OpenFOAM native MPI solver on it. I just did as your instruction, and got some problems. Can you tell me more details? Such as: 1. Make Zlib and Flex for Xeon Phi ----------This step is install Zlib and Flex on the host PC, am i right? 2. Set OpenFOAM bashrc/setting.sh to linux64Icc and INTEL MPI --i have done this step 3. Make wmake only 4. Add -mmic to wmake/rules/linux64ICC/{c, c++} -----i have done this 5. Compile OpenFOAM libraries. If compilation fails, add Zlib/Flex path to Make/options -------in directory ~/OpenFOAM/src, i run ./Allwmake, and got some errors, how did you add Zlib/Flex path to Make/options? Is the file Make/option refers to the file ~/OpenFOAM/OpenFOAM-2.2.0/src/OpenFOAM/Make/options? Thanks very much! Last edited by kimbaol; June 4, 2013 at 04:49. |
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June 3, 2013, 07:14 |
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#6 |
Senior Member
Vieri Abolaffio
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Dear Asaijo.
thanks for sharing your results. really interesting, and I'm impressed by them. --- also, for the sake of comparison, are you using the standard fvscheme and fvsolution? thanks in advance, i'd love to put my hands on one of those beauties... Last edited by sail; June 3, 2013 at 07:17. Reason: haven't read accurately enough what whas written by the OP |
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September 13, 2013, 01:18 |
Is 5110p really worth it?
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#7 |
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Asaijo, can you tell me how the performance using maximum processor core without xeon phi and with xeon phi, i want to know if Xeon Phi really worth it.
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October 15, 2013, 14:13 |
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#8 |
Senior Member
Robert
Join Date: Sep 2010
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Update:
The 'ld' linker has a problem with the .o files being compiled with -mmic flag. If I get rid of the -mmic flag, the ld command does not give the error. Of course, this is not what we want to do. Do I need to set ld architecture somehow??? I ran into the following " could not read symbols: File in wrong format" problem while trying to compile using the steps in the first post (I am on step 5, and I did add zlib and flex to Make/options to get rid of those errors). I went into the OSspecific/POSIX/ directory to compile it manually, but it made no difference. ld -r -o /home/lordvon/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64IccDPOpt/lib/libOSspecific.o Make/linux64IccDPOpt/sigFpe.o Make/linux64IccDPOpt/sigSegv.o Make/linux64IccDPOpt/sigInt.o Make/linux64IccDPOpt/sigQuit.o Make/linux64IccDPOpt/sigStopAtWriteNow.o Make/linux64IccDPOpt/sigWriteNow.o Make/linux64IccDPOpt/regExp.o Make/linux64IccDPOpt/timer.o Make/linux64IccDPOpt/fileStat.o Make/linux64IccDPOpt/POSIX.o Make/linux64IccDPOpt/cpuTime.o Make/linux64IccDPOpt/clockTime.o Make/linux64IccDPOpt/memInfo.o Make/linux64IccDPOpt/fileMonitor.o Make/linux64IccDPOpt/printStack.o ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) Make/linux64IccDPOpt/sigFpe.o: could not read symbols: File in wrong format make: *** [/home/lordvon/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64IccDPOpt/lib/libOSspecific.o] Error 1 I am using Red Hat Enterprise Linux Server release 6.4 (Santiago) Please help! sigFpe.o compiled fine, by the way via: SOURCE=signals/sigFpe.C ; icpc -std=c++0x -Dlinux64 -DWM_DP -wd327,654,819,1125,1476,1505,1572 -O2 -no-prec-div -DNoRepository -IlnInclude -I. -I/home/lordvon/OpenFOAM/OpenFOAM-2.2.2/src/OpenFOAM/lnInclude -I/home/lordvon/OpenFOAM/OpenFOAM-2.2.2/src/OSspecific/POSIX/lnInclude -fPIC -mmic -c $SOURCE -o Make/linux64IccDPOpt/sigFpe.o Last edited by lordvon; October 15, 2013 at 16:26. |
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October 20, 2013, 04:58 |
Cannot compile
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#9 |
New Member
Dennis
Join Date: Oct 2013
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Hi everyone,
First of all I would like to say thank you for sharing the information. I have a problem compiling OpenFOAM to work on Xeon Phi. After that I added -mmic to the c and c++ file in wmake/rules/linux64Icc/, the compilation fails and I receive this error message everywhere in the log: icpc: command line error: option '-xHost' not supported If I remove -mmic everything works fine, anyone know that the problem is ? |
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October 24, 2013, 14:20 |
cpu comparison
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#10 |
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May be I am wrong, by I will try compare results. There is some data
http://www.hector.ac.uk/cse/distribu...am/node17.html and from topic starter Xeon Phi for 50 time steps grid size - 90^3 - 175^3 best time - 200s - 1500 s Hectors 4 core of AMD 2.8GHz dual-core Opteron 5 time steps grid size - 100^3 - 200^3 time - 795s - 8800 s Hectors 1024 core of AMD 2.8GHz dual-core Opteron 40 time steps grid size - 200^3 time - 1490 s So, single Xeon Phi card for OpenFOAM is compatible with 1024 core cluster (for this benchmark) |
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May 12, 2014, 02:58 |
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#11 |
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Hi, i have done step 1 and 2..
how to do the third step? 3. Make wmake only |
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May 15, 2014, 22:27 |
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#12 |
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Hi, i got an error while doing these steps:
Code:
# CentOS 6.5 # OpenFoam 2.2.2 2. change etc/bashrc export WM_COMPILER=Icc export WM_MPLIB=INTEL_MPI 3. clean old compilation source etc/bashrc wcleanAll ; wcleanLnIncludeAll ; wcleanMachine 4a. add -mmic edit wmake/rules/linux64ICC/c cFLAGS = $(GFLAGS) $(cWARN) $(cOPT) $(cDBUG) $(LIB_HEADER_DIRS) -fPIC -mmic 4b. add -mmic edit wmake/rules/linux64ICC/c++ c++FLAGS = $(GFLAGS) $(c++WARN) $(c++OPT) $(c++DBUG) $(ptFLAGS) $(LIB_HEADER_DIRS) -fPIC -mmic 4c. remove -xHost (conflict with -mmic) vim wmake/rules/linux64Icc/c++Opt c++OPT = -O2 -no-prec-div 5. build for XeonPhi ./Allwmake Code:
icpc -std=c++0x -Dlinux64 -DWM_DP -wd327,654,819,1125,1476,1505,1572 -O2 -no-prec-div -DNoRepository -I/root/OpenFOAM/OpenFOAM-2.2.2/src/finiteVolume/lnInclude -ItractionDisplacementCorrectionStress -I../solidDisplacementFoam -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.2.2/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.2.2/src/OSspecific/POSIX/lnInclude -fPIC -mmic -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64IccDPOpt/tractionDisplacementCorrectionFvPatchVectorField.o Make/linux64IccDPOpt/solidEquilibriumDisplacementFoam.o -L/root/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64IccDPOpt/lib \ -lfiniteVolume -lOpenFOAM -ldl -L/lib -lm -o /root/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64IccDPOpt/bin/solidEquilibriumDisplacementFoam x86_64-k1om-linux-ld: cannot find -lfiniteVolume x86_64-k1om-linux-ld: cannot find -lOpenFOAM make[2]: *** [/root/OpenFOAM/OpenFOAM-2.2.2/platforms/linux64IccDPOpt/bin/solidEquilibriumDisplacementFoam] Error 1 make[2]: Leaving directory `/root/OpenFOAM/OpenFOAM-2.2.2/applications/solvers/stressAnalysis/solidEquilibriumDisplacementFoam' make[1]: *** [solidEquilibriumDisplacementFoam] Error 2 make[1]: Target `application' not remade because of errors. make[1]: Leaving directory `/root/OpenFOAM/OpenFOAM-2.2.2/applications/solvers/stressAnalysis' make: *** [stressAnalysis] Error 2 make: Target `application' not remade because of errors. |
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May 17, 2014, 15:06 |
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#13 |
Retired Super Moderator
Bruno Santos
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Greetings to all!
@kokizzu: I don't have access to a Xeon Phi, so I have no experience with it. Nonetheless, I have a lot of experience building OpenFOAM from source code, so here's what I can say regarding your latest post: when build OpenFOAM, usually the very first error that occurs is the one that tells the whole story. If you run Allwmake like this: Code:
./Allwmake > log.make 2>&1 Best regards, Bruno
__________________
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May 18, 2014, 07:31 |
undefined reference to `__intel_sse4_atol'
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#14 |
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Hi, I'm building OpenFOAM for Intel MIC (Xeon Phi), but i got this error:
Code:
icpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -xHost -O2 -no-prec-div -DNoRepository -I.. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/twoPhaseMixture/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/interfaceProperties/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/incompressible/turbulenceModel -I/root/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/fvOptions/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/sampling/lnInclude -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64IccDPOpt/porousInterFoam.o -L/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib \ -ltwoPhaseMixture -linterfaceProperties -ltwoPhaseProperties -lincompressibleTransportModels -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lmeshTools -lfvOptions -lsampling -lOpenFOAM -ldl -L/lib -lm -o /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/bin/porousInterFoam ld: warning: libimf.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libtwoPhaseMixture.so, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libtwoPhaseMixture.so, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libtwoPhaseMixture.so, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libtwoPhaseMixture.so, not found (try using -rpath or -rpath-link) /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libtriSurface.so: undefined reference to `__intel_sse4_atol' Code:
vim etc/bashrc export WM_COMPILER=Icc export WM_MPLIB= vim wmake/rules/linuxIcc/c cFLAGS = $(GFLAGS) $(cWARN) $(cOPT) $(cDBUG) $(LIB_HEADER_DIRS) -KPIC -mmic vim wmake/rules/linuxIcc/c++ c++FLAGS = $(GFLAGS) $(c++WARN) $(c++OPT) $(c++DBUG) $(ptFLAGS) $(LIB_HEADER_DIRS) -KPIC -mmic vim wmake/rules/linuxIcc/c++Opt c++OPT = -O2 -no-prec-div source etc/bashrc ./Allwmake the libimf.so was found here Code:
/opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/mic/libimf.so /opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/ia32/libimf.so /opt/intel/composer_xe_2013_sp1.1.106/compiler/lib/intel64/libimf.so /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/libimf.so /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/ia32/libimf.so /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64/libimf.so or should i run Code:
/opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars_arch.sh mic Last edited by kokizzu; May 18, 2014 at 07:44. Reason: more information |
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May 18, 2014, 14:20 |
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#15 | |
Retired Super Moderator
Bruno Santos
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Try running the last command like this instead:
Code:
source /opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars_arch.sh mic Beyond this, it does look like you're reaching the step #6 on the first post by asaijo: Quote:
Code:
cd $FOAM_SOLVERS/multiphase/interFoam/porousInterFoam mpiicpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -xHost -O2 -no-prec-div -DNoRepository -I.. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/twoPhaseMixture/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/interfaceProperties/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/incompressible/turbulenceModel -I/root/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/fvOptions/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/sampling/lnInclude -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64IccDPOpt/porousInterFoam.o -L/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib \ -ltwoPhaseMixture -linterfaceProperties -ltwoPhaseProperties -lincompressibleTransportModels -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lmeshTools -lfvOptions -lsampling -lOpenFOAM -ldl -L/lib -lm -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/ -o /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/bin/porousInterFoam
Last edited by wyldckat; May 18, 2014 at 14:33. Reason: not "intel64", it's "mic" |
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May 23, 2014, 16:32 |
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#16 |
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Hi, I've tried that, but still the same errors occured, when I added
Code:
-I/opt/intel/impi/4.1.3.049/mic/include/ Code:
wclean mpi wmake libso mpi wmakeLnInclude: linking include files to ./lnInclude Making dependency list for source file UIPread.C could not open file mpi.h for source file UIPread.C due to No such file or directory Making dependency list for source file UOPwrite.C could not open file mpi.h for source file UOPwrite.C due to No such file or directory Making dependency list for source file UPstream.C could not open file mpi.h for source file UPstream.C due to No such file or directory Making dependency list for source file PstreamGlobals.C could not open file mpi.h for source file PstreamGlobals.C due to No such file or directory SOURCE=UOPwrite.C ; mpiicpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -xHost -O2 -no-prec-div -DNoRepository -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64IccDPOptINTEL_MPI/UOPwrite.o SOURCE=UIPread.C ; mpiicpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -xHost -O2 -no-prec-div -DNoRepository -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64IccDPOptINTEL_MPI/UIPread.o SOURCE=UPstream.C ; mpiicpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -xHost -O2 -no-prec-div -DNoRepository -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64IccDPOptINTEL_MPI/UPstream.o SOURCE=PstreamGlobals.C ; mpiicpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -xHost -O2 -no-prec-div -DNoRepository -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64IccDPOptINTEL_MPI/PstreamGlobals.o ld: skipping incompatible /opt/intel/impi/4.1.3.049/mic/lib/libmpigc4.so when searching for -lmpigc4 ld: skipping incompatible /opt/intel/impi/4.1.3.049/mic/lib/libmpigc4.a when searching for -lmpigc4 ld: cannot find -lmpigc4 make: *** [/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/dummy/libPstream.so] Error 1 If I tried without using MPI, it shows something like this: Code:
ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) Make/linux64IccDPOpt/sigFpe.o: could not read symbols: File in wrong format make: *** [/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libOSspecific.o] Error 1 Hi, thanks for replying, here's my full configuration for the last error: Code:
yum install boost-devel cd ~/OpenFOAM/OpenFOAM-2.3.0 # edit etc/bashrc export WM_COMPILER=Icc export WM_MPLIB= source etc/bashrc # edit wmake/rules/linux*Icc/c cFLAGS = $(GFLAGS) $(cWARN) $(cOPT) $(cDBUG) $(LIB_HEADER_DIRS) -fPIC -mmic -I/opt/intel/impi/4.1.3.049/mic/include/ -I/opt/crtdc/micgnu/include/ # edit wmake/rules/linux*Icc/c++ c++FLAGS = $(GFLAGS) $(c++WARN) $(c++OPT) $(c++DBUG) $(ptFLAGS) $(LIB_HEADER_DIRS) -fPIC -mmic -I/opt/intel/impi/4.1.3.049/mic/include/ -I/opt/crtdc/micgnu/include/ # edit wmake/rules/linux64Icc/c++Opt c++OPT = -O2 -no-prec-div # edit wmake/rules/linux64Icc/c++ CC = mpiicpc -std=c++0x # edit wmake/rules/linuxIA64Icc/c++ CC = mpiicpc # edit wmake/rules/linuxIcc/c++ CC = mpiicpc -std=c++0x # edit wmake/rules/*Icc/c # edit wmake/rules/*Icc/c++ # add on LINK_LIBS -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/ -L/opt/crtdc/micgnu/lib/ source /opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars_arch.sh mic source /opt/intel/impi/4.1.3/mic/bin/mpivars.sh ./Allwmake > errors.log 2>&1 & tail -f errors.log Last edited by wyldckat; May 26, 2014 at 10:23. Reason: merged 3 posts that were a few minutes apart |
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May 24, 2014, 05:05 |
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#17 | |
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Quote:
Code:
cd ~/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX mkdir Make/linux64IccDPOpt/ SOURCE=signals/sigFpe.C ; icpc -std=c++0x -Dlinux64 -DWM_DP -wd327,654,819,1125,1476,1505,1572 -O2 -no-prec-div -DNoRepository -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/containers/Lists/UList/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/containers/Lists/UList/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/bools/bool/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/pTraits -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/ints/label/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/direction/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/chars/char/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/ints/int/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/strings/word/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/strings/string/ -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/primitives/hashes/Hasher/ -fPIC -mmic -c $SOURCE -o Make/linux64IccDPOpt/sigFpe.o -I../../OpenFOAM/primitives/ints/uLabel -I../../OpenFOAM/primitives/ints/uint -I../../OpenFOAM/db/error -I../../OpenFOAM/db/IOstreams/Sstreams -I../../OpenFOAM/db/IOstreams/IOstreams -I../../OpenFOAM/primitives/Scalar/scalar -I../../OpenFOAM/primitives/Scalar/floatScalar -I../../OpenFOAM/primitives/Scalar -I../../OpenFOAM/primitives/VectorSpace -I../../OpenFOAM/primitives/Scalar/doubleScalar -I../../OpenFOAM/primitives/strings/fileName -I../../OpenFOAM/primitives/strings/keyType -I../../OpenFOAM/primitives/Swap -I../../OpenFOAM/containers/Lists/List -I../../OpenFOAM/primitives/contiguous -I../../OpenFOAM/db/IOstreams/token -I../../OpenFOAM/memory/refCount -I../../OpenFOAM/db/typeInfo -I../../OpenFOAM/global/debug -I../../OpenFOAM/db/runTimeSelection/construction -I../../OpenFOAM/memory/autoPtr -I../../OpenFOAM/containers/HashTables/HashTable -I../../OpenFOAM/memory/Xfer -I../../OpenFOAM/containers/Lists/FixedList -I../../OpenFOAM/primitives/hashes/Hash -I../../OpenFOAM/primitives/strings/wordRe -I../../OpenFOAM/containers/LinkedLists/user -I../../OpenFOAM/containers/LinkedLists/accessTypes/LList -I../../OpenFOAM/containers/LinkedLists/linkTypes/SLListBase -I../../OpenFOAM/containers/Lists/PtrList -I../../OpenFOAM/memory/tmp -I../../OpenFOAM/containers/LinkedLists/accessTypes/LPtrList -I../../OpenFOAM/containers/Lists/IndirectList -I../../OpenFOAM/containers/Lists/UIndirectList -I../../OpenFOAM/containers/Lists/BiIndirectList -I../../OpenFOAM/global/JobInfo -I../../OpenFOAM/db/dictionary -I../../OpenFOAM/db/dictionary/entry -I../../OpenFOAM/containers/LinkedLists/accessTypes/ILList -I../../OpenFOAM/containers/LinkedLists/accessTypes/UILList -I../../OpenFOAM/containers/LinkedLists/linkTypes/DLListBase -I../../OpenFOAM/db/IOstreams/Tstreams -I../../OpenFOAM/primitives/strings/lists -I../../OpenFOAM/db/dictionary/primitiveEntry -I../../OpenFOAM/db/IOstreams/StringStreams -I../../OSspecific/POSIX/cpuTime -I../../OpenFOAM/include -I../../OpenFOAM/primitives/ints/long -I../../OpenFOAM/db/IOstreams Code:
ld -r -o /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libOSspecific.o Make/linux64IccDPOpt/sigFpe.o Make/linux64IccDPOpt/sigSegv.o Make/linux64IccDPOpt/sigInt.o Make/linux64IccDPOpt/sigQuit.o Make/linux64IccDPOpt/sigStopAtWriteNow.o Make/linux64IccDPOpt/sigWriteNow.o Make/linux64IccDPOpt/regExp.o Make/linux64IccDPOpt/timer.o Make/linux64IccDPOpt/fileStat.o Make/linux64IccDPOpt/POSIX.o Make/linux64IccDPOpt/cpuTime.o Make/linux64IccDPOpt/clockTime.o Make/linux64IccDPOpt/memInfo.o Make/linux64IccDPOpt/fileMonitor.o Make/linux64IccDPOpt/printStack.o ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) Make/linux64IccDPOpt/sigFpe.o: could not read symbols: File in wrong format make: *** [/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libOSspecific.o] Error 1 Code:
SOURCE=signals/sigFpe.C ; mpiicpc -std=c++0x -Dlinux64 -DWM_DP -wd327,525,654,819,1125,1476,1505,1572 -O2 -no-prec-div -DNoRepository -DFOAM_USE_INOTIFY -IlnInclude -I. -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/root/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude -fPIC -mmic -I/opt/intel/impi/4.1.3.049/mic/include/ -I/opt/crtdc/micgnu/include/ -c $SOURCE -o Make/linux64IccDPOpt/sigFpe.o |
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May 28, 2014, 01:22 |
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#18 | |
New Member
Join Date: Sep 2013
Posts: 12
Rep Power: 13 |
Since the "-L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/" doesn't work at all..
we're adding all ".so" files on "cFLAGS" part on the "c" and "c++" file, for example: Quote:
some warning disappear, but some warning still shows up: Code:
x86_64-k1om-linux-ld: warning: libirng.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/intel64/libPstream.so, not found (try using -rpath or -rpath-link) x86_64-k1om-linux-ld: warning: libdynamicMesh.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libautoMesh.so, not found (try using -rpath or -rpath-link) x86_64-k1om-linux-ld: warning: liblagrangian.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libautoMesh.so, not found (try using -rpath or -rpath-link) x86_64-k1om-linux-ld: warning: libfileFormats.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libautoMesh.so, not found (try using -rpath or -rpath-link) ... x86_64-k1om-linux-ld: warning: libdsmc.so, needed by /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libutilityFunctionObjects.so, not found (try using -rpath or -rpath-link) *snip* very long long mpiipcp command *snip* /root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/postCalc.o: In function `Foam::tryCalc(Foam::argList const&, Foam::Time const&, Foam::fvMesh const&)': (.text+0x1520): undefined reference to `Foam::calc(Foam::argList const&, Foam::Time const&, Foam::fvMesh const&)' any possible solution for solving those errors? |
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May 28, 2014, 03:51 |
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#19 |
New Member
Join Date: Sep 2013
Posts: 12
Rep Power: 13 |
at last.. (/^__^)/
this one works: wmake/rules/linux64Icc/c Code:
.SUFFIXES: .c .h cWARN = cc = icc include $(RULES)/c$(WM_COMPILE_OPTION) cFLAGS = -I/opt/intel/impi/4.1.3.049/mic/include/ -I/opt/crtdc/micgnu/include/ $(GFLAGS) $(cWARN) $(cOPT) $(cDBUG) $(LIB_HEADER_DIRS) -fPIC \ -mmic -I/usr/include -Wl,/opt/crtdc/micgnu/lib/libz.so ctoo = $(WM_SCHEDULER) $(cc) $(cFLAGS) -c $$SOURCE -o $@ LINK_LIBS = -Wl,-rpath-link,/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/,-rpath-link,/opt/crtdc/micgnu/lib,-rpath-link,/root/OpenFOAM/OpenFOAM-2.3.0/platf orms/linux64IccDPOpt/lib/intel64/,-rpath-link,/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/ -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/ -L /opt/crtdc/micgnu/lib/ $(cDBUG) -L$(IA32ROOT)/lib LINKLIBSO = $(cc) $(cFLAGS) -shared LINKEXE = $(cc) $(cFLAGS) -Xlinker --add-needed -Xlinker -z -Xlinker nodefs Code:
.SUFFIXES: .C .cxx .cc .cpp c++WARN = -wd327,525,654,819,1125,1476,1505,1572 CC = mpiicpc -std=c++0x include $(RULES)/c++$(WM_COMPILE_OPTION) ptFLAGS = -DNoRepository c++FLAGS = -I/opt/intel/impi/4.1.3.049/mic/include/ -I/opt/crtdc/micgnu/include/ $(GFLAGS) $(c++WARN) $(c++OPT) $(c++DBUG) $(ptFLAGS) $(LIB_HEADER_DIRS) -fPIC \ -mmic -I/usr/include -Wl,/opt/crtdc/micgnu/lib/libz.so Ctoo = $(WM_SCHEDULER) $(CC) $(c++FLAGS) -c $$SOURCE -o $@ cxxtoo = $(Ctoo) cctoo = $(Ctoo) cpptoo = $(Ctoo) LINK_LIBS = -Wl,-rpath-link,/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/,-rpath-link,/opt/crtdc/micgnu/lib,-rpath-link,/root/OpenFOAM/OpenFOAM-2.3.0/platf orms/linux64IccDPOpt/lib/intel64/,-rpath-link,/root/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/ -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic/ -L /opt/crtdc/micgnu/lib/ $(c++DBUG) -L$(IA64ROOT)/lib LINKLIBSO = $(CC) $(c++FLAGS) -shared -Xlinker --add-needed -Xlinker --no-as-needed LINKEXE = $(CC) $(c++FLAGS) -Xlinker --add-needed -Xlinker --no-as-needed |
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June 9, 2014, 00:31 |
OpenFOAM2.3.0 on Xeon Phi with OpenMPI1.6.5 (could not read symbols)
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#20 |
New Member
Join Date: Jun 2014
Posts: 2
Rep Power: 0 |
Dear All,
I would be very grateful if you tell me how you specifically fixed the following problem: wmake libso mpi '/home/manumachu/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/openmpi-1.6.5/libPstream.so' is up to date. + OSspecific/POSIX/Allwmake Found <sys/inotify.h> -- enabling inotify for file monitoring. ld -r -o /home/manumachu/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libOSspecific.o Make/linux64IccDPOpt/sigFpe.o Make/linux64IccDPOpt/sigSegv.o Make/linux64IccDPOpt/sigInt.o Make/linux64IccDPOpt/sigQuit.o Make/linux64IccDPOpt/sigStopAtWriteNow.o Make/linux64IccDPOpt/sigWriteNow.o Make/linux64IccDPOpt/regExp.o Make/linux64IccDPOpt/timer.o Make/linux64IccDPOpt/fileStat.o Make/linux64IccDPOpt/POSIX.o Make/linux64IccDPOpt/cpuTime.o Make/linux64IccDPOpt/clockTime.o Make/linux64IccDPOpt/memInfo.o Make/linux64IccDPOpt/fileMonitor.o Make/linux64IccDPOpt/printStack.o ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) ld: Make/linux64IccDPOpt/sigFpe.o: Relocations in generic ELF (EM: 181) Make/linux64IccDPOpt/sigFpe.o: could not read symbols: File in wrong format make: *** [/home/manumachu/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPOpt/lib/libOSspecific.o] Error 1 Best Regards Manredd |
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