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mpich Examples and Code Snippets
def build_recursive_hd_all_reduce(input_tensors, red_op, un_op=None):
"""Construct a subgraph for recursive halving-doubling all-reduce.
The recursive halving-doubling algorithm is described in
(Thakur et al., 2015).
The concept is to arran
Community Discussions
Trending Discussions on mpich
QUESTION
I am in the process of learning MPI in fortran, and so I've been writing a bunch of small functions that do simple tasks in MPI to get a good handle on it. However, halfway through, i began getting this error when trying to compile
...ANSWER
Answered 2022-Apr-15 at 07:23implicit none
must appear before include 'mpif.h'
That being said, this is very error prone, and you should at least use
QUESTION
I am trying to run a CMakeLists.txt file on a (48h) fresh ubuntu 20.04.3 install. I keep getting the following error when running cmake .
ANSWER
Answered 2022-Feb-14 at 23:57Use CMAKE_PREFIX_PATH variable to set search path. Best practice is set that variable in command line interface:
QUESTION
Updated:
I am trying to install repast hpc 2.3.1 on my MacBook Pro with M1 processor, however I run into the following issue. I am following the Install.txt instructions included in the package. The issue now occurs when I try to use ./install rhpc
I get the following errors, which seem to stem from the GridComponents.o file failing to find the DBL_MAX variable and marking it as undeclared:
ANSWER
Answered 2022-Feb-10 at 14:26I've outlined all the required fixes (including the DBL_MAX fix) here: https://github.com/Repast/repast.hpc/issues/7. With those in place, the zombies and rumor demo models work on macOS on an M1 Max laptop.
All that said, and as an aside, we typically do our repast hpc and repast4py development work on a Linux VM running under Parallels or VMWare Fusion on a Mac. This is because that more closely matches the cluster or HPC environments we ultimately run the models on.
QUESTION
I'm trying to use execute a basic C++ script (here). I believe I've installed the HDF5 library correctly using:
sudo apt install libhdf5-dev
When I first tried to compile the code using:
g++ hdf5_simple.cpp -lhdf5 -lhdf5_cpp -o hdf5_simple
I got:
hdf5_simple.cpp:3:10: fatal error: H5Cpp.h: No such file or directory
Simple enough, I try:
g++ -I/usr/include/hdf5/serial/ hdf5_simple.cpp -lhdf5 -lhdf5_cpp -o hdf5_simple
And it complies with no issues, but when I try to run it is get:
...ANSWER
Answered 2022-Jan-18 at 18:21Try this:
QUESTION
I have a program that I would like to compile with CMake + make but using two different MPI distributions, OpenMPI and MPICH.
In Ubuntu, I have both installed; these are all the compiler wrappers I have installed:
...ANSWER
Answered 2021-Dec-28 at 05:57Setting -DMPI_ROOT=
or -DMPI_HOME=
didn't work for me. It still uses the default in my system (OpenMPI).
What worked was to set -DMPI_EXECUTABLE_SUFFIX=.mpich
, option which I found near the end of the documentation: https://cmake.org/cmake/help/latest/module/FindMPI.html.
QUESTION
I am writing a python program that establishes a ssh connection to a server. For this I am using fabric (fabfile.org).
When I connect to the server via ssh in a terminal, I get my $PATHs set. When I connect to the server via fabric in my python program, $PATHs are missing...
- Where does bash load the $PATHs when I connect via terminal?
- How do I manage that fabric does the same?
Thanks in advance!
edit:
this is what I get, when I run echo -e ${PATH//:/\\n}
:
SSH via Terminal:
...ANSWER
Answered 2021-Nov-27 at 01:24I found the solution:
I got to run source /etc/profile
with fabric in order to get my correct PATHs.
Found out by reading: https://www.gnu.org/software/bash/manual/bash.html#Bash-Startup-Files
QUESTION
I am trying to install an open-source parallel finite-element code called TACS and available at this github repository. To comply with the indicated prerequisites, I followed the instructions at this github repository, which allowed me to install SuiteSparse and METIS on Windows with precompiled BLAS/LAPACK DLLs. For the MPI, I installed both the Intel MPI Library and Open MPI through Cygwin. The final step should be to compile running make
, however this command is not directly available in Windows 10. As a consequence, I explored the options suggested in this question, unfortunately without success. I feel at a dead end, any help will be appreciated.
Please have a look below at my attempts. I am mainly a Windows user and I don't know much of compiling programs using Makefile
. My current understanding is that the Makefile
that I am trying to compile is written for Linux and whatever GNU compiler for Windows I use will not work because of the different syntax needed. Please correct me if I am wrong. What I can't understand is why I get errors also when I try to compile with Ubuntu Bash for Windows 10 (last attempt of the list below).
nmake
Running the Developer Command Prompt for VS 2019 as administrator, I typed nmake -f Makefile
in TACS base directory and I got Makefile.in(28) : fatal error U1001: syntax error : illegal character '{' in macro Stop.
make
Running Windows Command Prompt as administrator with C:\ProgramData\chocolatey\bin
at the top of PATH
environment variable, I typed make
in TACS base directory and I got
ANSWER
Answered 2021-Oct-03 at 14:08I can't answer but maybe I can orient you.
First nmake
is not make. It will not work with any makefile not written specifically as an nmake makefile. And it's only available on Windows. So, best to just forget it exists.
Second, it's important to understand how make works: rules in makefiles are a combination of targets/prerequisites, and a recipe. The recipe is not in "makefile" syntax, it's a shell script (batch file). So make works in tandem with the shell, to run commands. Which shell? On POSIX systems like GNU/Linux and MacOS it's very simple: a POSIX shell; by default /bin/sh
.
On Windows systems it's much less simple: there are a lot of options. It could be cmd.exe
. It could be PowerShell. It could be a POSIX shell, that was installed by the user. Which one is chosen by default, depends on how your version of make
was compiled. That's why you see different behaviors for different "ports" of make
to Windows.
So, if you look at the makefiles you are trying to use you can see they are unquestionably written specifically for a POSIX system and expect a POSIX shell and a POSIX environment. Any attempt to use a version of make
that invokes cmd.exe
as its default shell will fail immediately with syntax errors ("" was unexpected at this time.).
OK, so you find a version of make that invokes a POSIX shell, and you don't get that error anymore.
But then you have to contend with another difference: directory separators. In Windows they use backslash. In POSIX systems, they use forward slash and backslash is an escape character (so it's not just passed through the shell untouched). If you are going to use paths in a POSIX shell, you need to make sure your paths use forward slashes else the shell will remove them as escape characters. Luckily, most Windows programs accept forward slashes as well as backslashes as directory separators (but not all: for example cmd.exe
built-in tools do not).
Then you have to contend with the Windows abomination known as drive letters. This is highly problematic for make
because to make
, the :
character is special in various places. So when make sees a line like C:/foo:C:/bar
its parser will get confused, and you get errors. Some versions of make
compiled for Windows enable a heuristic which tries to see if a path looks like a drive letter or not. Some just assume POSIX-style paths. They can also be a problem for the POSIX shell: many POSIX environments on Windows map drive letters to standard POSIX paths, so C:\foo
is written as /c/foo
or /mnt/c/foo
or something else. If you are adding paths to your makefile you need to figure out what the right mapping, if any, is and use that.
That's not even to start discussing the other differences between POSIX and Windows... there are so many.
From what you've shown above, this project was not written with any sort of portability to Windows in mind. Given the complexity of this, that's not surprising: it takes a huge amount of work. So you have these options that I can see:
- Port it yourself to be Windows-compatible
- Try to get it working inside cygwin (cygwin is intended to be a POSIX-style environment that runs on Windows)
- Try to get it working in WSL
- Install a virtual machine using VMWare, VirtualBox, etc. running a Linux distribution and build and run it there
Unfortunately I don't know much about the pros and cons of these approaches so I can't advise you as to the best course.
The route I chose, long long ago, was to get rid of Windows entirely and just use GNU/Linux. But of course that won't be possible for everyone :).
QUESTION
I am implementing an application using MPICH (sudo apt get mpich) on Linux (Ubuntu).
My current solution looks like this:
...ANSWER
Answered 2021-Sep-29 at 12:29The "user" keyword can be used to assign logical cores manually. Hence, one can write:
QUESTION
I'm using FreeBSD 13, and trying to compile (successfully) and run (un-succesfully) a simple minimal MPI program
...ANSWER
Answered 2021-Sep-22 at 02:24Seemed to have been a bug, I just saw it was fixed by FreeBSD folks.
See https://cgit.freebsd.org/ports/commit/?id=fd490a171c3da0d7bcb9a5f3ee3b4b46075dfa9e
QUESTION
I have a class that creates a new MPI_Datatype
in its constructor and then deletes it in its destructor. However, the presence of the deletion of the custom datatype somehow triggers the calling of MPI_Finalize()
within the destructor.
ANSWER
Answered 2021-Aug-24 at 20:07@VictorEijkhout suggested the following solution in his comments. The idea is to create a communicator object which calls MPI_Init
and MPI_Finalize
in its constructor and destructor, then pass that object to other functions or classes for further manipulation.
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