I would like to install PETSc library with Intel compilers, OpenMP, MPI, MKL. I am not sure how to properly create configure file. I have intel parallel studio xe 2017 installed on my computer. I checked ./configure --help in PETSc directory for options, but there is plenty of them. I don't how should I match it with Intel-mkl-link-line-advisor.
Anyone did this before?
I use these build lines for my Intel build. Unfortunately I stumbled uppon your questio while trying to fix my own problem (which is probably caused by something else) but this build worked liek a charm for over 2 years.
Of course you'll have to change the PETSc dir to your source directory. The 'tee's are so that I can run a script that generates all the build I need (with differing compilers, MPI implementations, debug/opt, etc) and still have logs from each build on separete files.
./configure --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-blas-lapack-dir=/opt/intel/mkl/lib/intel64/ --with-debugging=1 PETSC_ARCH=linux-intel-dbg all test | tee linux-intel-dbg/configure.log
make PETSC_DIR=~/opt/petsc/ PETSC_ARCH=linux-intel-dbg all | tee linux-intel-dbg/make.log
make PETSC_DIR=~/opt/petsc/ PETSC_ARCH=linux-intel-dbg test | tee linux-intel-dbg/test.log
make PETSC_DIR=~/opt/petsc/ PETSC_ARCH=linux-intel-dbg streams NPMAX=8 | tee linux-intel-dbg/streams.log
Related
Background: I compile bitcoind on one system but run it on another. When I compiled bitcoind 0.19.1 some time back using the following method, I was able to run bitcoind and bitcoin-cli on the target system without issue. I think.
./autogen.sh
./configure --disable-wallet --disable-tests --disable-bench --disable-gui --enable-util-tx=no --prefix=$HOME/bitcoind/x64 --exec-prefix=$HOME/bitcoind/x64
make && make install
Today I compiled v0.20.0 using the same method. If I run ./bitcoind -version on the system I compiled the binary it runs fine, but if I take the binary to my target system I get the following error:
./bitcoind: error while loading shared libraries: libboost_filesystem.so.1.67.0: cannot open shared object file: No such file or directory
The binary seemed to be portable last time, and the pre-compiled binary I download from the Bitcoin Core team runs fine.
Note that on the target system libboost-filesystem-dev and libboost-filesystem1.67-dev are not installed, this is likely the source of my error. That said, running the pre-compiled binary from the Core team runs, so why doesn't mine?
Can someone help me understand if I did something wrong or if I need to add ./configure flags to make the binary more portable? Specifically what I likely did differently than the core developers that made my binary fail where theirs worked?
EDIT 1: Running ./configure --enable-static or ./configure LDFLAGS=-static does not result in a portable binary either.
Also note that installing libboost-filesystem library with apt does fix the error.
Thanks to Andrew Chow for his helpful answer to this on the bitcoind StackExchange. I needed to build the depends as per the depends documentation. Since I'm building for the same platform I'll be running on, I can run make in the depends directory with no arguments except -j2 which uses two cores. Change the number to however many cores you want to commit to the compile.
cd depends
make -j2
cd ..
./autogen.sh
./configure --prefix=$PWD/depends/x86_64-pc-linux-gnu
make -j2 && make install
I am running Arch Linux and trying to build a project in Qt however, Qt spits the following error:
/opt/cuda/include/crt/host_config.h:129: error: #error -- unsupported GNU version! gcc versions later than 7 are not supported!
I have already tried a suggestion from a previous Stack Overflow post found here:
CUDA incompatible with my gcc version
I did not use the exact command as my cuda is located in /opt/cuda/bin/gcc. I did the same command for g++. However, the terminal outputs that these files are already linked. I did confirm this by going to the actual file and looking at it's properties.
Can someone please suggest a solution to my issue?
I managed to do so usung this two lines, this will update the symbolic links of cuda to gcc7
ln -s /usr/bin/gcc-7 /usr/local/cuda/bin/gcc
ln -s /usr/bin/g++-7 /usr/local/cuda/bin/g++
The issue comes from cuda-10.0/targets/x86_64-linux/include/crt/host_config.h in the main CUDA-10 directory tree. The target for your architecture was placed in /opt.
Some posts recommend faking the inequality
if __GNUC__ > 7
to say
if __GNUC__ > 8
but that is a bad idea. Using
make 'NVCCFLAGS=-m64 -D__GNUC__=7' -k
is permissible in some trivial cases, but still fundamentally the same bad hack.
You probably have alternates on your system which has constructed symbolic links pointing to the version 8 gnu tool chain files. That's why you get an indication version 7 is already installed.
You can learn how to modify your alternates for just your developer users BUT NOT for root or any system admin accounts. You may want to remember how to switch back and forth between 7 and 8 so you only use 7 when actually needed, since many other things may be tested only with 8.
If that doesn't work for you, you can build gcc-7 from source. The preparatory system admin work includes a dnf install, a build from source, an install of 7.4 gnu compiler, and a set up of paths for CUDA development only. If you have gnu gcc and g++ version 8 installed with the appropriate standard libraries and it works, the version 7 compiler can be installed with relative ease.
Browse and find the nearest mirror listed on https://gcc.gnu.org/mirrors.html and then copy the link location for gcc-7.4.0.tar.xz and place it in the shell variable u like this example.
u="http://mirrors.concertpass.com/gcc/releases/gcc-7.4.0/gcc-7.4.0.tar.xz"
Then you can do the rest as commands.
sudo dnf install libmpc-devel
cd
mkdir -p scratch
cd scratch
wget -O - "$u" |tar Jxf -
cd gcc-7.4.0
mkdir build
cd build
../configure --prefix=/usr/local/gcc-7
make
sudo bash -c "cd \"`pwd`\"; make install"
Then you execute this in the shells and tools you develop with. Do NOT put this in the system login apparatus or in .bashrc or .bash_profile, for the same reason as above. Other things may be tested with version 8 only. Instead place them in your development environment where they belong.
LD_LIBRARY_PATH=/usr/local/gcc-7/lib64:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/usr/local/gcc-7/lib:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/usr/local/cuda-10.0/NsightCompute-1.0/host/linux-desktop-glibc_2_11_3-glx-x64/Plugins:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/usr/local/cuda-10.0/NsightCompute-1.0/target/linux-desktop-glibc_2_11_3-glx-x64:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/usr/local/cuda-10.0/targets/x86_64-linux/lib/stubs:$LD_LIBRARY_PATH
PATH=/usr/local/gcc-7/bin:$PATH
PATH=/usr/local/cuda-10.0/bin:$PATH
PATH=$HOME/big/cuda.samples/NVIDIA_CUDA-10.0_Samples/bin/x86_64/linux/release:$PATH
On install path of websphere MQ/java/lib/jdbc>make oracle
I am getting below error
xlc: not found
I am not sure if xlc is installed in my machine. My machine is AIX 6.1. But I can find xlcpp in my machine. how to proceed?Is there any way to create switch file?
If I execute $ /usr/ccs/lib/cpp -help
I am getting
1506-173 (W) Option help is not valid. Enter xlc for list of valid options.
how to proceed?
/usr/ccs/lib/cpp is not the XL C/C++ for AIX compiler, it is the C Pre-Processor which ships as part of AIX. The XL C/C++ for AIX compiler is a separate Licensed Program Product for which licenses must be separately purchased.
If you have XL C/C++ for AIX installed, you would find the /usr/vac/bin/xlc and /usr/vacpp/bin/xlc++ commands installed on your system. You can also check for the filesets vac.C and vacpp.cmp.core using the lslpp command:
lslpp -L vac.C vacpp.cmp.core
Dwayne has it mostly right but I believe xlc++ also has a version of xlc. I see in your other question that you have xlcpp so perhaps what you need to do is add /usr/vacpp/bin to your PATH.
I also tend to use grep with lslpp:
lslpp -ch | grep vac
should tell you which xlc, xlcpp, etc you have installed.
HTH
My programming experience is about 1 year of C/C++ experience from high school, but I did my research and wrote a simple program with OpenCL a few months ago. I was able to compile and run this on an Apple computer relatively easily with g++ and the --framework option. Now I'm on my Ubuntu machine and I have no idea how to compile it. The correct drivers have been downloaded along with ATI's Stream SDK (I have an ATI Radeon HD5870). Any help would be appreciated!
Try
locate libOpenCL.so
If it is in one of the standard directories (most likely /usr/lib, or /usr/local/lib) you need to replace "--framework OpenCL" with "-lOpenCL". If g++ cannot find the lib you can tell g++ to look in a specific directory by adding "-L/path/to/library".
I wish I had my Linux to be more helpful... It is probably best if you redownload the ati-stream-sdk, after extracting it, open the Terminal and "cd /path/to/extracted/files"; in that directory execute make && sudo make install
make you probably know this from windows, this compiles, whatever needs to be compiled
&& chains commands together, the following commands will only be executed if the first command succeeded
sudo make install this will put the files in the expected places (sudo executes a command with superuser priviledges, you will have to enter your password)
Hope that helps.
You might be missing the dynamic libraries from the dynamic linker configuration.
Search for where the libraries are. Most likely /usr/lib, or /usr/local/lib.
Make sure the path location is also configured at one of these places:
LD_LIBRARY_PATH - you can set it in you environment shell, like .bashrc
/etc/ld.so.conf - you will need to call ldconfig to update the cache and it requires root access to change the file.
Reason
Aside from #bjoernz, my system can't find the libOpenCL.so file
It's because the correct file directory is missing
After searchig over the internet, I found out that libOpenCL.so file can provided by ocl-icd-opencl-dev package
Solution
You just need to install the package mentioned above by typing into cmd
sudo apt update
sudo apt install ocl-icd-opencl-dev
Therefore, libOpenCL.so can be found under /usr/lib/x86_64-linux-gnu/ folder
My System Information
OS: Ubuntu 16.04 LTS
GPU: NVIDIA GeForce GTX 660
GPU Driver: nvidia-375
OpenCL: 1.2
Reference:
[1] How to install libOpenCL.so on ubuntu
[2] How to set up OpenCL in Linux
I'm trying to build an application from source in windows that requires some Unix tools. I think it's the apparently standard ./configure; make; make install (there's no INSTALL file). First I tried MinGW but got confused that there was no bash, autoconf, m4, or automake exes in \bin. I'm sure I missed something obvious but I installed Cygwin anyways just to move forward. For some reason when I run
sh configure.sh
I get:
platform unix
compiler cc
configuration directory ./builds/unix
configuration rules ./builds/unix/unix.mk
My OS has identity problems. Obviously the makefile is all wrong since I'm not on unix but win32. Why would the configure script think this? I assume it has something to do with Cygwin but if I remove that I can't build it at all. Please help; I'm very confused.
Also is it possible to build using MinGW? What's the command for bash and is mingw32-make the same as make? I noticed they're different sizes.
Everything is fine. When you are inside CygWin, you are basically emulating an UNIX. sh runs inside CygWin, and thus identifies the OS correctly as Unix.
Have a look at GCW - The Gnu C compiler for Windows
Also, you might be interested in this help page, that goes into some detail about the minimal system (MSYS), such as how to install, configure et. c.
That should help you get bash, configure and the rest to work for MinGW as well.
From the Cygwin home page
Cygwin is a Linux-like environment for Windows. It consists of two parts:
A DLL (cygwin1.dll) which acts as a Linux API emulation layer providing substantial Linux API functionality.
A collection of tools which provide Linux look and feel.
Since configure is using the Cygwin environment, it is interacting against the emulation layer and so it is just like it's working on a Unix environment.
Have you tried building the application and seeing if it works?