I'm really naive and know almost nothing about MPI. I'm trying to do some analyses in R that require Rmpi package. But I'm stuck with this problem:
Version of R 3.2.5 (x64) on Windows 10
I installed MPICH2
Added proper addresses on PATH environment variables
Successfully set smpd and mpiexec registration
Installed Rmpi using Rgui
If I call Rmpi using normal Rterm it is loaded. But when I try
mpi.spawn.Rslaves(), it returns :
Error in mpi.spawn.Rslaves() : Spawning is not implemented. Please use mpiexec with Rprofile.*
so I run on prompt :
mpiexec -n 2 "C:\Program Files\R\R-3.2.5\bin\x64\Rterm.exe" --no-save –q
So far so good.
I can load any package without problems but when it comes to call Rmpi library I get this error message:
Aborting: mpi appplication on DESKTOP-0UI5TAT is unable to connect to the smpd manager on (null):57362 error 1722
job aborted:
[ranks] message
[0] fatal error
Fatal error in MPI_Init: Other MPI error, error stack:
MPI_Init(argc_p=0x0018FA44, argv_p=0x0018FA48) failed
The RPC server is unavailable. (errno 1722)*
Even using the more recent MS-MPI software, when I call Rmpi it simply starts a new line without any prompt > and so it remains
I deep searched on the whole internet and tried several options but it's still not working
you have to create a shortcut that Rstudio is lunched by mpiexec ,otherwise the Rstudio doesn't know Mpi
follow instruction here
http://www.stats.uwo.ca/faculty/yu/Rmpi/
Related
The Jim Hester YouTube video video looks like a potentially really helpful way to put breakpoints in Rcpp code that passes some variables in unexpected ways. However, when I follow the start up directions (Rstudio console copied below) it fails with a message that is not helpful to a new user of lldb.
gcn#GCN-MacBook-Pro-7 ISIMIPData % R -d lldb
(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
(lldb) run
error: process exited with status -1 (attach failed (Not allowed to attach to process. Look in the console messages (Console.app), near the debugserver entries when the attached failed. The subsystem that denied the attach permission will likely have logged an informative message about why it was denied.))
(lldb)
The Console.app output that I could find is not very useful.
A later post post describes an updated process but it too fails in a similar way. I'm using Rstudio version 1.4.1717 with R version 4.1.
I have tried running the Openmdao paraboloid tutorial as well as benchmarks and I consistently receive the same error which reads as following:
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash
---------------------------------------------------------------------
MPI_abort was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59.
NOTE: invoking MPI_ABORT causes MPI to kill all MPI processes.
you may or may not see output from other processes, depending on exactly when Open MPI kills them.
I don't understand why this error is occurring and what I can do to be able to run OpenMDAO without getting this error. Can you please help me with this?
Something has not gone well with your PETSc install. Its hard to debug that from afar though. It could be in your MPI install, or your PETSc install, or your petsc4py install. I suggest not install PETSc or PETSc4Py through pip though. I've had mixed success with that. Both can be installed from source without tremendous difficulty.
However, to run the tutorials you don't need to have PETSc installed. You could remove those packages and the tutorials will run correctly in serial for you
I am trying to run a Julia program using Gurobi solver on Windows.
I have already set up my GUROBI_HOME in windows as C:\gurobi701\win64.
Here is the error message in Atom:
error msg
I have done the following in Julia interactive shell:
Pkg.add("Gurobi")
also
Pkg.update()
Also, I checked whether or not my gurobi license file is not properly set up by running their example:
> gurobi_cl C:\gurobi701\win64\examples\data\coins.lp
The output seems fine: output for gurobi command line
What is the possible error here?
Thanks a lot for help!!!
This is the first time I have tried to connect R and Tableau.
I have downloaded and installed Rserve successfully but every time I try to start Rserve is get this warning:
Starting Rserve...
"C:\Users\SIMON~1.HAR\DOCUME~1\R\WIN-LI~1\3.1\Rserve\libs\x64\Rserve.exe"
Warning message:
running command '"C:\Users\SIMON~1.HAR\DOCUME~1\R\WIN-LI~1\3.1\Rserve\libs\x64\Rserve.exe" ' had status 127
I have been searching for days and couldn't find any fix.
The Rserve() function is trying to start an application (Rserve.exe) and failed. There's a couple of things you can do.
Go to the "C:\Users\SIMON~1.HAR\DOCUME~1\R\WIN-LI~1\3.1\Rserve\libs\x64\" file directory and try loading the exe yourself, troubleshoot from there.
use the run.Rserve() function instead of Rserve(). This will use your current R session to start the Rserve server. This means the exe doesn't need to be run. This worked well for me because I am working in an environment where I don't enough privileges to run the exe. It does mean that your R session can't do anything else while the server is running, but you can always load up 2 sessions at the same time.
I'm attempting to run a parallel job in R using snow. I've been able to run extremely similar jobs with no trouble on older versions of R and snow. R package dependencies prevent me from reverting.
What happens: My jobs terminate at the parRapply step, i.e., the first time the nodes have to do anything short of reporting Sys.info(). The error message reads:
Error in checkForRemoteErrors(val) :
3 nodes produced errors; first error: cannot open the connection
Calls: parRapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Specs: R 2.14.0, snow 0.3-8, RedHat Enterprise Linux Client release 5.6. The snow package has been built on the correct version of R.
Details:
The following code appears to execute fine:
cl <- makeCluster(3)
clusterEvalQ(cl,library(deSolve,lib="~/R/library"))
clusterCall(cl,function() Sys.info()[c("nodename","machine")])
I'm an end-user, not a system admin, but I'm desperate for suggestions and insights into what could be going wrong.
This cryptic error appeared because an input file that's requested during program execution wasn't actually present. Each node would attempt to load this file and then fail, but this would result only in a "cannot open the connection" message.
What this means is that almost anything can cause a "connection" error. Incredibly annoying!