similar to: R with ATLAS avoids Linux cpu affinity

I've attempted to use the optimized GotoBLAS2 library with a freshly compiled R-2.11.1 patched on 64-bit Ubuntu 10.4. (See details below). When I run this version of R, the timings are not different than the original install, and only one core is used in test computations. Can someone point out my error? Thanks. --Dale Details ... I'm running the 64-bit version of Ubuntu 10.04 on my 2

Dirk suggested I move this thread over here. I am trying to get a multithreaded (multi CPU) version of ATLAS working with R, and have been unable, thus far, to get it working. Has anyone gotten an multithreaded version of ATLAS working on Debian (64 bit)? I've tried this: apt-get source atlas -t unstable cd atlas-3.8.3 DEFAULTS=n fakeroot debian/rules custom but it is APPEARING to only

Hi, I'm relatively new to R on Ubuntu (moving from Windows), and I'm trying to get GotoBLAS2 working. I installed (from a CRAN mirror) the pre-built binaries of R (which, as far as I know, is compiled as a shared library) on Ubuntu 10.10 using apt-get install r-base r-base-dev I successfully built GotoBLAS2 from source, copied the library to /usr/lib and created s symbolic link from

Dirk Eddelbuettel <edd <at> debian.org> writes: > One last follow-up. Debian's Atlas maintainer has started to work in the > OpenGoto packaging. There will be proper Goto packages now that the license > is better, but it may take a while. It took years to get Atlas packaged > 'right' so don;t expect anything too soon. The gotoblas2-helper package is >

Hello, According to the docs, vcpupin will use either cgroups or sched_setaffinity to pin vcpu threads to cpus. How is this decision made? I observe differences even on different hosts featuring the same version of libvirtd (1.3.1): on one host vcpupin affects cpuset.cpus (cgroup), and on the other it affects vcpu threads affinity (observed through taskset). Thanks, Nikos -------------- next

Hi, GridEngine (http://gridengine.sunsource.net, aka. SGE) is an opensource batch system for clusters. They have an integration with SSH: http://gridengine.sunsource.net/project/gridengine/howto/qrsh_ssh.html The idea is that instead of using a modified rsh/rshd, they wanted to OpenSSH. However, in order to provide full job control, they need to add a few hooks in OpenSSH. Question: - Is it OK

Hello, This simple SVD calculation (commands are copied immediately below) crashes on my Ubuntu machine (R 2.13.0). However it worked fine with R.12 and Ubuntu 10.04, and it also works fine on my Windows 7 machine with R 2.13, so I suspect there's a problem with (my?) Ubuntu and / or R. I'm using the R distribution that is accessible with Ubuntu's repositories manager, I am not

Rhelpers: I recently installed the 64-bit version of R on my Debian system, and afterwards was asked if it was compiled using ATLAS. Is there a way to test to see if R is using ATLAS? --j

On Wed, Sep 05, 2018 at 03:48:45PM +0300, Nikos Anastopoulos wrote: >Hello, > >According to the docs, vcpupin will use either cgroups or sched_setaffinity >to pin vcpu threads to cpus. How is this decision made? >I observe differences even on different hosts featuring the same version of >libvirtd (1.3.1): on one host vcpupin affects cpuset.cpus (cgroup), and on >the other it

Hi, everybody. I notice debian packages for Ubuntu on CRAN are missing "libRblas.so" and I'm trying to find out why. Why do I care? We are working in an hpc project in a CentOS Linux cluster. That led me to the question of "which BLAS is fastest?" Dirk E referred me this morning to the R admin manual. The standard R compilation creates a shared blas library libRblas.so

Hi all, I managed to at least compile R-patched (2002-01-08) against MKL 5.1 (not beta). The release notes for MKL said that the libraries are threaded, and the test codes needed to be linked against the pthread library. Therefore I added -lpthread flag in config.site for R-patched, and the compile went through. However, when I did make check, it choked on a call to La.eigen, complaining that

On Mon, Aug 24, 2015 at 11:29 AM, Bj?rn-Helge Mevik <b.h.mevik at usit.uio.no> wrote: > arnaud gaboury <arnaud.gaboury at gmail.com> writes: > >> - Intel MKL: this is part of Intel Parallel Studio and is a paid >> software. Now, there is the MKL package distributed by >> Revolutionanalytics, but I am not certain how this can be distributed >> for free. Is

G'day. I'm having a little trouble getting Gridengine 5.3 running properly on a cluster using Centos 3.3. Everything appears okay, but my jobs hang in the queue with the gridengine complaining that node is overloaded, but there is nothing (unusual) running on the node and the load is 0. Has anyone else run into similar problems? -geoff

Hi, with small matrices eigen works as expected: > eigen(cbind(c(1,4),c(4,7)), only.values = TRUE) $values [1] 9 -1 $vectors NULL > eigen(cbind(c(1,4),c(4,7))) $values [1] 9 -1 $vectors [,1] [,2] [1,] 0.4472136 -0.8944272 [2,] 0.8944272 0.4472136 > eigen(cbind(c(1,-1),c(1,-1))) $values [1] -3.25177e-17+1.570092e-16i -3.25177e-17-1.570092e-16i $vectors

http://bugzilla.mindrot.org/show_bug.cgi?id=1070 Summary: Enchancement: Integration with GridEngine Product: Portable OpenSSH Version: 4.1p1 Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P2 Component: sshd AssignedTo: bitbucket at mindrot.org ReportedBy:

On Mon, Aug 24, 2015 at 1:42 PM, Dirk Eddelbuettel <edd at debian.org> wrote: > > On 24 August 2015 at 11:43, arnaud gaboury wrote: > | On Mon, Aug 24, 2015 at 11:29 AM, Bj?rn-Helge Mevik > | <b.h.mevik at usit.uio.no> wrote: > | > arnaud gaboury <arnaud.gaboury at gmail.com> writes: > | > > | >> - Intel MKL: this is part of Intel Parallel Studio

The OpenMPI package that ships with CentOS 5.1 does not seem to be compiled with torque support. It does, however, seem to be compiled with gridengine and slurm support. Would it be possible to get this changed?

I want to build R optimized, with either MKL, OpenBLAS or ATLAS. My OS: Fedora 22 Hardware: CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 8 Thread(s) per core: 2 Vendor ID: GenuineIntel Model name: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz I am a little confused when it comes to choose a method and would like to hear your experiences. If I am right, I have 3 possibilities: -

Hello. I know almost nothing about Linux, so I apologize if the answer to this is obvious. I am trying to compile R with ATLAS (successfully compiled 3.9.24 on Ubuntu 10.04 64 bit). I configured with: ./configure --enable-R-shlib --enable-BLAS-shlib --with-blas="-L/usr/local/atlas/lib -lf77blas -latlas" --with-lapack="-L/usr/local/atlaslib -llapack -lcblas" --with-x and I

Hello. I know almost nothing about Linux, so I apologize if the answer to this is obvious. I am trying to compile R with ATLAS (successfully compiled 3.9.24 on Ubuntu 10.04 64 bit). I configured with: ./configure --enable-R-shlib --enable-BLAS-shlib --with-blas="-L/usr/local/atlas/lib -lf77blas -latlas" --with-lapack="-L/usr/local/atlaslib -llapack -lcblas" --with-x and I