EDIT 2 I tried to reinstall OpenMPI with sudo apt-get install --reinstall openmpi-bin libopenmpi-dev and with sudo apt-get purge openmpi-bin libopenmpi-dev sudo apt-get install openmpi-bin libopenmpi-dev but none of them had the desired effect, library still links against intel libraries. Improve this question. Alexandros Markopoulos. Alexandros Markopoulos Alexandros Markopoulos 83 1 1 gold badge 1 1 silver badge 4 4 bronze badges. Could you edit the question and add which intel libs did you install and how did you install them?
Also the output of which mpicc. Add a comment. Active Oldest Votes. Improve this answer. I added more details into my question.
I added other details into my question. The three categories are: End user Generally, these are parameters that are required for correctness, meaning that a user may need to set these just to get their MPI application to run correctly.
Application tuner Generally, these are parameters that can be used to tweak MPI application performance. This even includes parameters that control resource exhaustion levels e. But, really -- they're tuning parameters. Building Open MPI from a tarball defaults to building an optimized version.
There is no need to do anything special. This allows Open MPI to be built in a different directory than where its source code resides helpful for multi-architecture builds. Some versions of make support parallel builds. The example above shows GNU make's " -j " option, which specifies how many compile processes may be executing at any given time.
See the source code access pages for more information. Changing this build behavior is controlled via command line options to Open MPI's configure script. Similarly, you can build both static and shared libraries by simply specifying --enable-static and not specifying --disable-shared , if desired. Including components in libraries: Instead of building components as DSOs, they can also be "rolled up" and included in their respective libraries e. This is controlled with the --enable-mca-static option.
Automake uses a tightly-woven set of file timestamp-based dependencies to compile and link software. This will result in files with incorrect timestamps, and Automake degenerates into undefined behavior. Two solutions are possible: Ensure that the time between your network filesystem server and client s is the same.
This can be accomplished in a variety of ways and is dependent upon your local setup; one method is to use an NTP daemon to synchronize all machines to a common time server. Build on a local disk filesystem where network timestamps are guaranteed to be synchronized with the local build machine's time. Then you can run configure , make , and make install.
Open MPI should then build and install successfully. Ensure that when you run a new shell, no output is sent to stdout. For example, if the output of this simple shell script is more than just the hostname of your computer, you need to go check your shell startup files to see where the extraneous output is coming from and eliminate it : 1 2 3! This is usually an indication that configure succeeded but really shouldn't have.
See this FAQ entry for one possible cause. Open MPI uses a standard Autoconf "configure" script to probe the current system and figure out how to build itself. One of the choices it makes it which compiler set to use. However, this is easily overridden on the configure command line.
Note that you can include additional parameters to configure , implied by the " Unexpected or undefined behavior can occur when you mix compiler suites in unsupported ways e. Open MPI uses a standard Autoconf configure script to set itself up for building. Note that the flags you specify must be compatible across all the compilers. In particular, flags specified to one language compiler must generate code that can be compiled and linked against code that is generated by the other language compilers.
These codes will be incompatible with each other, and Open MPI will build successfully. The above command line will pass " -m64 " to all four compilers, and therefore will produce 64 bit objects for all languages. Bad Things then happen. Currently the only workaround is to disable shared libraries and build Open MPI statically. For Googling purposes, here's an error message that may be issued when the build fails: 1 2 3 4 xlc: - command option --whole-archive is not recognized - passed to ld xlc: - command option --no-whole-archive is not recognized - passed to ld xlc: - file libopen-pal.
The easiest way to work around them is simply to use the latest version of the Oracle Solaris Studio 12 compilers. Apply Sun patch The PathScale compiler authors have identified a bug in the v3. With PathScale 3. Here's a proposed solution from the PathScale support team from July : The proposed work-around is to install gcc Newer versions of the compiler 4. We don't anticipate that this will be much of a problem for Open MPI users these days our informal testing shows that not many users are still using GCC 3.
To build support for high-speed interconnect networks, you generally only have to specify the directory where its support header files and libraries were installed to Open MPI's configure script. You can specify where multiple packages were installed if you have support for more than one kind of interconnect — Open MPI will build support for as many as it can. You tell configure where support libraries are with the appropriate --with command line switch.
NOTE: Up through the v1. In the v1. You can verify that configure found everything properly by examining its output — it will test for each network's header files and libraries and report whether it will build support or not for each of them.
Examining configure 's output is the first place you should look if you have a problem with Open MPI not correctly supporting a specific network type. Last supported in the v1. Slurm support is built automatically; there is nothing that you need to do. XGrid support is built automatically if the XGrid tools are installed. The method for configuring it is slightly different between Open MPI v1.
For Open MPI v1. After Open MPI is installed, you should see two components named gridengine. Component versions may vary depending on the version of Open MPI 1. In general, the procedure is the same building support for high-speed interconnect networks , except that you use --with-tm. Because of this, you may run into linking errors when Open MPI tries to create dynamic plugin components for TM support on some platforms.
How did you install Open MPI? Using apt-get install? Add a comment. Active Oldest Votes. Improve this answer. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name.
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