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Nbody6++GPU-Dec2017
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‎.gitignore

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# Prerequisites
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*.d
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# Object files
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*.o
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*.ko
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*.obj
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*.elf
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# Linker output
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*.ilk
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*.map
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*.exp
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# Precompiled Headers
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*.gch
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*.pch
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# Libraries
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*.lib
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*.a
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*.la
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*.lo
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# Shared objects (inc. Windows DLLs)
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*.dll
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*.so
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*.so.*
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*.dylib
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# Executables
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*.exe
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*.out
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*.app
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*.i*86
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*.x86_64
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*.hex
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*.avx
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*.sse
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*.mpi
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*.gpu
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*.b1m
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# Debug files
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*.dSYM/
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*.su
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*.idb
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*.pdb
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# Kernel Module Compile Results
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*.mod*
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*.cmd
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.tmp_versions/
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modules.order
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Module.symvers
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Mkfile.old
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dkms.conf
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‎Makefile

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#
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# Makefile for NBODY6++ June 2003 R.Sp., Changed by Long Wang on Aug 20, 2014
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#
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# Please use:
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# make
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# make install
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#
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RESULT = nbody6++
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INSTALLDIR = /usr/local
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EXTRATOOLS = nb6++dumpb2a libinitial.so libnb6out3.so nb6++snapshot
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ifeq ("x", "x $(EXTRATOOLS)")
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EXTRAOBJS = installtools
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endif
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VPATH=./build
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$(RESULT) :
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$(MAKE) -C ./build
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clean:
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rm -f ./build/*.o ./build/*.so ./build/$(RESULT) $(EXTRATARGET)
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install: $(RESULT) $(EXTRAOBJS)
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@[ -d $(INSTALLDIR)/bin ] || mkdir $(INSTALLDIR)/bin
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@[ -d $(INSTALLDIR)/share ] || mkdir $(INSTALLDIR)/share
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@[ -d $(INSTALLDIR)/share/doc ] || mkdir $(INSTALLDIR)/share/doc
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cp ./build/$(RESULT) $(INSTALLDIR)/bin
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cp ./doc/nbody6++_manual.pdf $(INSTALLDIR)/share/doc/
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installtools:
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@[ -d $(INSTALLDIR)/bin ] || mkdir $(INSTALLDIR)/bin
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@[ -d $(INSTALLDIR)/include ] || mkdir $(INSTALLDIR)/include
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@[ -d $(INSTALLDIR)/lib ] || mkdir $(INSTALLDIR)/lib
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cp ./build/nb6++dumpb2a $(INSTALLDIR)/bin
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cp ./build/nb6++snapshot $(INSTALLDIR)/bin
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cp ./include/initial.h $(INSTALLDIR)/include
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cp ./build/libinitial.so $(INSTALLDIR)/lib
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cp ./include/nb6out3.h $(INSTALLDIR)/include
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cp ./build/libnb6out3.so $(INSTALLDIR)/lib
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uninstall:
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rm -f $(INSTALLDIR)/bin/$(RESULT)
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rm -f $(INSTALLDIR)/lib/libinitial.so $(INSTALLDIR)/lib/libnb6out3.so
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rm -f $(INSTALLDIR)/share/doc/nbody6++_manual.pdf
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rm -f $(INSTALLDIR)/bin/nb6++dumpb2a $(INSTALLDIR)/bin/nb6++snapshot

‎Makefile.in

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#
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# Makefile for NBODY6++ June 2003 R.Sp., Changed by Long Wang on Aug 20, 2014
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#
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# Please use:
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# make
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# make install
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#
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RESULT = nbody6++@RESULT@
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INSTALLDIR = @prefix@
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EXTRATOOLS = nb6++dumpb2a libinitial.so libnb6out3.so nb6++snapshot
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ifeq ("x@EXTRARESULT@", "x $(EXTRATOOLS)")
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EXTRAOBJS = installtools
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endif
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VPATH=./build
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$(RESULT) @EXTRARESULT@:
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$(MAKE) -C ./build
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clean:
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rm -f ./build/*.o ./build/*.so ./build/$(RESULT) $(EXTRATARGET)
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install: $(RESULT) $(EXTRAOBJS)
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@[ -d $(INSTALLDIR)/bin ] || mkdir $(INSTALLDIR)/bin
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@[ -d $(INSTALLDIR)/share ] || mkdir $(INSTALLDIR)/share
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@[ -d $(INSTALLDIR)/share/doc ] || mkdir $(INSTALLDIR)/share/doc
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cp ./build/$(RESULT) $(INSTALLDIR)/bin
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cp ./doc/nbody6++_manual.pdf $(INSTALLDIR)/share/doc/
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installtools: @EXTRARESULT@
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@[ -d $(INSTALLDIR)/bin ] || mkdir $(INSTALLDIR)/bin
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@[ -d $(INSTALLDIR)/include ] || mkdir $(INSTALLDIR)/include
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@[ -d $(INSTALLDIR)/lib ] || mkdir $(INSTALLDIR)/lib
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cp ./build/nb6++dumpb2a $(INSTALLDIR)/bin
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cp ./build/nb6++snapshot $(INSTALLDIR)/bin
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cp ./include/initial.h $(INSTALLDIR)/include
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cp ./build/libinitial.so $(INSTALLDIR)/lib
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cp ./include/nb6out3.h $(INSTALLDIR)/include
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cp ./build/libnb6out3.so $(INSTALLDIR)/lib
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uninstall:
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rm -f $(INSTALLDIR)/bin/$(RESULT)
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rm -f $(INSTALLDIR)/lib/libinitial.so $(INSTALLDIR)/lib/libnb6out3.so
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rm -f $(INSTALLDIR)/share/doc/nbody6++_manual.pdf
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rm -f $(INSTALLDIR)/bin/nb6++dumpb2a $(INSTALLDIR)/bin/nb6++snapshot

‎README

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Welcome to use Nbody6++, which is the parallel version of Nbody6.
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Please send Email to [email protected] if you find some problems during using the code.
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---------------------------------------------------------------------
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To install Nbody6++, please use:
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./configure [options]
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make
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make install
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The configure has several optional features, please use
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./configure --help
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to check these features.
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----------------------
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Some basice features:
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--Install path:
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The default install path is /usr/local, if you want to change another path, please use:
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./configure --prefix=[YOURPATH]
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Replace [YOURPATH] to the full path that you want to install Nbody6++.
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There will be "bin", "doc", ["include", "lib"] created in your install path.
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--GPU:
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The GPU support is enabled in default case, if you want to disable GPU acceleration, please use:
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./configure --disable-gpu
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--MPI:
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The MPI is enabled in default case, if you want to disable MPI, please use:
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./configure --disable-mpi
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--AVX/SSE:
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The AVX is enable in default case, you can choose no AVX/SSE, SSE and AVX, the option is:
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./configure --enable-simd=[arg]
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Replace [arg] by "no", "sse", "avx".
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--HDF5 output format:
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The HDF5 is disabled in default case, if you want to enable it, please use:
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./configure --enable-hdf5
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--extra tools:
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There are some extra tools and libraries for reading conf.3 and do some basic analysis, the default case it's disabled, if you want to compile them, please use:
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./configure --enable-tools
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All these options can be used in the same time. For example:
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./configure --prefix=/opt/nbody6++ --enable-tools --enable-hdf5
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---------------------------------------------------------------------
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***Important notice:
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* When large NMAX is used, sometimes the segmentational fault happened after the simulation begin. This is due to the stack memory overflow. In this case, you should always run
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$ ulimit -s unlimited
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before the code is started in the same shell.
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Be careful that the "ulimit" only works for current shell, thus it's need to be used every time when a new shell is opened.
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You can put it in .bashrc or .bash_profile to always load it when a new shell is open.
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* In some Linux systems (e.g. Ubuntu), when the large NMAX is used, the compiling crash with the error:
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"*** R_X86_64_PC32 against symbol ***"
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This error is related to the memory model of the Linux system. The detail of memory model is shown in https://software.intel.com/en-us/node/579558
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The solution is to add the configure option "--enable-mcmodel=large"
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In this case, the code performance may slightly decrease compared with "mcmodel=medium/small"
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---------------------------------------------------------------------
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Please check doc/Nbody6++_manual.pdf for the detail description of Nbody6++
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‎README.local

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Note: simple desktop/laptop try:
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./configure --disable-mpi --disable-gpu [--disable-simd --disable-openmp]
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---------------------------------------------------
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March 2017, local psk compilation, or on laptop
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ssh to psk1 - psk4
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check module avail
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module load openmpi-x86_64
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make sure the CUDA environment is there, for example which nvcc
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if not load module or ask system manager, we need cuda, cuda-sdk, cudalib
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cuda 5.0 ie enough, higher is pk
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./configure --enable-simd=avx --disable-hdf5 --enable-mpi --enable-tools --enable-gpu --with-cuda --with-cuda_sdk --enable-mcmodel=large --enable-option-checking --with-par=1024k
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./configure --enable-simd=avx --disable-hdf5 --enable-mpi --enable-tools --enable-gpu --with-cuda --with-cuda_sdk --enable-option-checking --with-par=128k
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#### THE FOLLOWING configure WORKS
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./configure --enable-simd=avx --enable-hdf5 --enable-mpi --enable-tools --enable-gpu --with-cuda --with-cuda_sdk --enable-mcmodel=large --enable-option-checking --with-par=1m
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Configure example for laptop single core:
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./configure --disable-simd --disable-gpu --disable-mpi --with-par=128k
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check in ./build/Makefile these lines:
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FC = mpif77
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CXX = g++
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CC = gcc
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NVCC = nvcc
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For laptop use export FC = gfortran before configure; in build/Makefile the line GPU_FLAGS = -D GPU has
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to be commented out by #
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if FC is not correct, or if the configure fails with error message 'there is no GNU compiler" try:
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export FC=mpif77
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and rerun configure...
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---------------------------
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cp -p -i build/nbody6++.avx.gpu.mpi ../run-nnnn your run directory
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nbody6++
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--------------------------
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How to run the code if interactive parallel runs are allowed (and if the
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GPUs are on this local node)
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mpirun -n 2 ./nbody6++.avx.gpu.mpi < abbas.inp 1>> abbas.out 2>> abbas.err &
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--------------------------
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sources are in ./src/Main *.[fF] includes are in ./include *.h
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-------------------------
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to recompile few files )in Nbody6pp-master directory only it works)::
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rm build/myobject.o
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rm build/execfile (for example nbody6++.avx.mpi.gpu )
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make
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-----------------------
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NEW-27/03/2017
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before running configure use:
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module load mvapich2-x86_64
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use the following command before compiling the code:
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scl enable devtoolset-2 bash

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