User:Ppomorsk - Revision history

Ppomorsk: /* Software which I help maintain */

2019-11-06T20:48:00Z

‎Software which I help maintain

Ppomorsk: /* Important Pages */

2019-11-06T20:47:45Z

‎Important Pages

Ppomorsk at 14:18, 3 May 2019

2019-05-03T14:18:21Z

Ppomorsk: /* Install Octopus */

2018-01-04T22:16:58Z

‎Install Octopus

Ppomorsk: /* Install clFFT */

2018-01-04T22:12:42Z

‎Install clFFT

Ppomorsk: /* Octopus instructions */

2018-01-04T22:12:29Z

‎Octopus instructions

Ppomorsk: /* Octopus instructions */

2018-01-04T22:11:27Z

‎Octopus instructions

Ppomorsk at 22:09, 4 January 2018

2018-01-04T22:09:28Z

Ppomorsk: add global work check

2016-11-21T22:23:46Z

add global work check

Ppomorsk: /* Install CNVnator */

2016-07-16T13:31:31Z

‎Install CNVnator

← Older revision		Revision as of 20:48, 6 November 2019
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	[[User:Ppomorsk/Toward Exascale Simulations of 3D Radiative Transfer for Cloudy Atmospheres]]		[[User:Ppomorsk/Toward Exascale Simulations of 3D Radiative Transfer for Cloudy Atmospheres]]
−
−	~~== Software which I help maintain ==~~
−
−	*[[CPMD]]
−
−	*[[CUDA]]
−
−	*[[GCC]]
−
−	*[[NAMD]]
−
−	*[[OpenCL]]
−
−	*[[Python]]
−
−	*[[SIESTA]]
−
−	*[[XCrySDen]]
−
−	*[[MKL]]

	== Help Wiki stats ==		== Help Wiki stats ==

← Older revision		Revision as of 20:47, 6 November 2019
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	[[User:Ppomorsk/Toward Exascale Simulations of 3D Radiative Transfer for Cloudy Atmospheres]]		[[User:Ppomorsk/Toward Exascale Simulations of 3D Radiative Transfer for Cloudy Atmospheres]]
−
−	~~== Important Pages ==~~
−
−	*[[CUDA]]
−

	== Software which I help maintain ==		== Software which I help maintain ==

← Older revision		Revision as of 14:18, 3 May 2019
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	module load gsl/2.3		module load gsl/2.3
	./configure FC='ifort -mkl' CC='icc -mkl' CXX='icpc -mkl' --prefix=/home/ppomorsk/octopus-exec --enable-opencl --with-clblas-prefix=/home/ppomorsk/clblasinstall --with-clfft-prefix=/home/ppomorsk/clfftinstall		./configure FC='ifort -mkl' CC='icc -mkl' CXX='icpc -mkl' --prefix=/home/ppomorsk/octopus-exec --enable-opencl --with-clblas-prefix=/home/ppomorsk/clblasinstall --with-clfft-prefix=/home/ppomorsk/clfftinstall
		+
		+
		+
		+
		+
		+
		+	'''OpenSees''' (Open System for Earthquake Engineering Simulation) is a software framework for simulating the seismic response of structural and geotechnical systems. It has advanced capabilities for modeling and analyzing the nonlinear response of systems using a wide range of material models, elements, and solution algorithms. Website: [http://opensees.berkeley.edu/ opensees.berkeley.edu]
		+
		+	The "svn" and "make" steps are likely to take a long time. To avoid having to stay logged in for many hours while these steps run, you can use the "screen" utility. Please see this page for instructions: [[FAQ:_Logging_in_to_Systems,_Transferring_and_Editing_Files#How_can_I_suspend_and_resume_my_session.3F]].
		+
		+	'''Trunk (24mar2017)''' tested on orca running centos6 by preney@sharcnet.ca March 24, 2017. The compile is done with the GCC compiler and system TCL library.
		+
		+	=== Serial version ===
		+
		+	Starting in your home directory, run the following commands.
		+
		+	mkdir bin
		+	mkdir lib
		+	svn co svn://peera.berkeley.edu/usr/local/svn/OpenSees/trunk OpenSees
		+	cd OpenSees
		+	cp ./MAKES/Makefile.def.EC2-REDHAT-ENTERPRISE ./Makefile.def
		+
		+	Now edit Makefile.def so it has:
		+	LINKFLAGS = -rdynamic
		+	instead of
		+	LINKFLAGS = -rdynamic -Wl
		+	and also have
		+	CC++ = g++
		+	CC = gcc
		+	FC = gfortran
		+
		+	Then compile with:
		+	module purge
		+	module load gcc/5.1.0
		+	make
		+
		+	=== Parallel MPI version ===
		+
		+	Starting in your home directory, run the following commands.
		+
		+	mkdir bin
		+	mkdir lib
		+	svn co svn://peera.berkeley.edu/usr/local/svn/OpenSees/trunk OpenSees
		+	cd OpenSees
		+	cp ./MAKES/Makefile.def.EC2-REDHAT-ENTERPRISE ./Makefile.def
		+
		+	Now edit Makefile.def so it has:
		+
		+	PROGRAMMING_MODE = DISTRIBUTED_MPI
		+	CC++ = mpiCC
		+	CC = mpicc
		+	FC = gfortran
		+
		+	and
		+	LINKFLAGS = -rdynamic
		+	instead of
		+	LINKFLAGS = -rdynamic -Wl
		+
		+	Then compile with:
		+
		+	module unload intel
		+	module unload openmpi
		+	module load gcc/5.1.0
		+	module load openmpi/gcc510-std/1.8.7
		+	make
		+
		+	You need to perform the same module operations before running the program with MPI.

@@ Line 233: / Line 233: @@
   module load fftw/3.3.6
   module load gsl/2.3
-  ./configure FC='ifort -mkl' CC='icc -mkl' CXX='icpc -mkl'  --prefix=/home/ppomorsk/test_compile/octopus-exec --enable-opencl --with-clblas-prefix=/home/ppomorsk/clblasinstall --with-clfft-prefix=/home/ppomorsk/clfftinstall
+  ./configure FC='ifort -mkl' CC='icc -mkl' CXX='icpc -mkl'  --prefix=/home/ppomorsk/octopus-exec --enable-opencl --with-clblas-prefix=/home/ppomorsk/clblasinstall --with-clfft-prefix=/home/ppomorsk/clfftinstall

@@ Line 219: / Line 219: @@
   git clone https://github.com/clMathLibraries/clFFT.git
   module load cuda/8.0.44
   module load fftw/3.3.6

@@ Line 210: / Line 210: @@
   module load cuda/8.0.44
   module load boost/1.60.0
   FC=ifort CC=icc CXX=icpc cmake ..  -DNetlib_BLAS_LIBRARY=$EBROOTOPENBLAS   -DNetlib_INCLUDE_DIRS=$EBROOTOPENBLAS/include -
   DCMAKE_INSTALL_PREFIX=~/clblasinstall -DBUILD_TEST:BOOL=OFF
   make
   make install
+ ln -s ~/clblasinstall/lib64 ~/clblasinstall/lib
 ln -s ~/clblasinstall/lib64 ~/clblasinstall/lib
 ==== Install clFFT ====
@@ Line 224: / Line 222: @@
   module load fftw/3.3.6
   module load boost/1.60.0
   FC=ifort CC=icc CXX=icpc cmake .. -DCMAKE_INSTALL_PREFIX=~/clfftinstall  -DOpenCL_LIBRARY=$CUDA_HOME/lib64/libOpenCL.so
@@ Line 235: / Line 232: @@
   module load fftw/3.3.6
   module load gsl/2.3
   ./configure FC='ifort -mkl' CC='icc -mkl' CXX='icpc -mkl'  --prefix=/home/ppomorsk/test_compile/octopus-exec --enable-opencl --with-clblas-prefix=/home/ppomorsk/clblasinstall --with-clfft-prefix=/home/ppomorsk/clfftinstall

← Older revision		Revision as of 22:11, 4 January 2018
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	make		make
	make install		make install
		+
		+	ln -s ~/clblasinstall/lib64 ~/clblasinstall/lib
		+
		+	==== Install clFFT ====
		+
		+	git clone https://github.com/clMathLibraries/clFFT.git
		+	module load cuda/8.0.44
		+	module load fftw/3.3.6
		+	module load boost/1.60.0
		+
		+	FC=ifort CC=icc CXX=icpc cmake .. -DCMAKE_INSTALL_PREFIX=~/clfftinstall -DOpenCL_LIBRARY=$CUDA_HOME/lib64/libOpenCL.so
		+
		+	==== Install Octopus ====
		+
		+	module load openblas/0.2.20
		+	module load cuda/8.0.44
		+	module load boost/1.60.0
		+	module load libxc/3.0.0
		+	module load fftw/3.3.6
		+	module load gsl/2.3
		+
		+	./configure FC='ifort -mkl' CC='icc -mkl' CXX='icpc -mkl' --prefix=/home/ppomorsk/test_compile/octopus-exec --enable-opencl --with-clblas-prefix=/home/ppomorsk/clblasinstall --with-clfft-prefix=/home/ppomorsk/clfftinstall

← Older revision		Revision as of 22:09, 4 January 2018
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	which-global-work		which-global-work
	USER=ppomorsk which-global-work		USER=ppomorsk which-global-work
		+
		+
		+	=== Octopus instructions ===
		+
		+	==== Install cblas ====
		+
		+	module load openblas/0.2.20
		+	module load cuda/8.0.44
		+	module load boost/1.60.0
		+
		+	FC=ifort CC=icc CXX=icpc cmake .. -DNetlib_BLAS_LIBRARY=$EBROOTOPENBLAS -DNetlib_INCLUDE_DIRS=$EBROOTOPENBLAS/include -
		+	DCMAKE_INSTALL_PREFIX=~/clblasinstall -DBUILD_TEST:BOOL=OFF
		+	make
		+	make install

← Older revision		Revision as of 22:23, 21 November 2016
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	This will produce the executable. In the future, run the above export LD_LIBRARY_PATH command to be able to run it.		This will produce the executable. In the future, run the above export LD_LIBRARY_PATH command to be able to run it.
		+
		+
		+	=== Checking global work location ===
		+	which-global-work
		+	USER=ppomorsk which-global-work

@@ Line 165: / Line 165: @@
 ===Install CNVnator===
 (load same modules as for root above)
   wget http://sv.gersteinlab.org/cnvnator/CNVnator_v0.3.zip