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Author Archives: pauljohn
Debian Wheezy multilib transition: caution
Here’s a cautionary heads up on the transition from ordinary to multilib Debian. I run Debian Wheezy amd64. Some 32 bit applications are installed, and somehow I came to a point where ia32libs wanted to update and transition me to … Continue reading
R package profiling with Google
I want to speed up R packages written with the Rcpp and RcppArmadillo packages. gprof is not an option because R is not compiled with -pg, and just re-compiling the shared libraries of the packages is insufficient. valgrind can generate … Continue reading
Posted in R
Tagged high performance computing, profiler
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fighting with sprof
$ export LD_PROFILE_OUTPUT=/tmp/oout $ export LD_PROFILE=`pwd`/Amelia.so $ mkdir -p /tmp/oout//home/pauljohn/R/x86_64-pc-linux-gnu-library/2.15/Amelia/libs/ $ env | grep LD OLDPWD=/home/pauljohn/R/x86_64-pc-linux-gnu-library/2.15/Amelia LD_LIBRARY_PATH=/home/pauljohn/R/x86_64-pc-linux-gnu-library/2.15/Amelia/libs LD_PROFILE=/home/pauljohn/R/x86_64-pc-linux-gnu-library/2.15/Amelia/libs/Amelia.so LD_PROFILE_OUTPUT=/tmp/oout After that $ R -f testfile.R If there is trouble, it looks like this: > library(Amelia) Loading required package: foreign Loading … Continue reading
Faster R: Things to not forget
We ask all the time, how to make R go faster, and there are a few basic tips and clear working examples, but except for that, it is confusing. We just have to test. It is not unique to R. … Continue reading
Posted in Uncategorized
Tagged fasterR, optimize, speed
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tar and ssh together to backup onto remote machine
On my laptop, I have working installs of some programs and I want to back them up as tar.gz files on a server that I can access via ssh. The disk on the server is formatted in windows NTFS. It … Continue reading
Posted in Uncategorized
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RedHat 6.3 updates
We have an external disk with RedHat 6.3 provided by tech support. We have to work from that base because it has the user ID system configured for the KU HOME domain. Otherwise, I would dump that and just use … Continue reading
Posted in Uncategorized
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Centos 6.3 64 bit
I just noticed my external disk for Centos was in 32 bit, and maybe we are safe to use 64. Installed a fresh Centos 6.3 and then tried to make a journal to summarize the updates/hassles. IN the process, I … Continue reading
Posted in Linux
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Cisco AnyConnect VPN on RedHat/Centos Enterprise Linux
I’ve just wasted several hours on configuring VPN for my university’s system. The University adopted Cisco AnyConnect, which is provided in a shell script “vpnsetup.sh”. There are several flaws in the script, however, which make this a relatively tough, confusing … Continue reading
Fighting through the LaTeX startup hassles
You kids know I’m not a Windows user, so I experience a different set of problems than you usually do. But the WinStat systems can be made to work, and the CRMDA systems can too. You just need to be … Continue reading
Posted in Uncategorized
Tagged Emacs, LatinModern, Linux, TexWorks, Windows
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New Linux System Setup: Don’t forget
For all users, put in place some protections and conveniences. In /etc/bash.bashrc or /etc/profile.d/safe.sh, add these alias lines: alias rm=’rm -i’ alias cp=’cp -i’ alias mv=’mv -i’ After that, the removal or destructive file copies will ask the user for … Continue reading