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Re: testfiles for c35b2 failed
lennart #20583 04/17/09 10:57 PM
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I'm aware of an NMR group that had a publication model close to that

Re: testfiles for c35b2 failed
lennart #20584 04/23/09 11:20 PM
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To Lennart:
Yes, CHARMM is a research tool for serious scientists that strive to know what they're doing, and making CHARMM "too easy" through things like "smart - in some situations - defaults" would encourage users to shoot themselves in the foot and blame CHARMM. Nevertheless, this principle doesn't justify the lamentable state of the documentation, nor CHARMM's general quirkiness. Just to name 2 examples: try to explain to a not-so-technical user why setting "FORMAT" under some conditions might break "CALC", or why "SYSTEM" calls with a lowercase variable in them only work when performed like this (mind the "back quotes"):
Code:
system "`echo shell_command @CHARMM_VARIABLE | awk '{print tolower($0)}'`"



That said, your point is taken; back to business.


To Sassy:
I have to agree with Rick. We had a cluster with a woefully obsolete version of the kernel and glibc in our lab, which we didn't wish to touch for "various reasons", so we:
1. compiled gmp, mpfr, and sufficiently recent versions of binutils and gcc from source in a user's home directory,
2. set appropriate environment variables to use the resulting utilities and libraries instead of the system's defaults,
3. compiled CHARMM,
4. copied the resulting CHARMM binary to a place where all nodes can see it (this works thanks to the fact that CHARMM is statically linked from A to Z).

Here's a "processed" version of my shell history when doing so. Please use common sense to point to the proper directories. So, after untarring all the tarballs from
http://gmplib.org/
http://www.mpfr.org/
http://www.gnu.org/software/binutils/
http://gcc.gnu.org/
in /home/user/install and cd-ing to /home/user/install, I did
Code:
######## Compile libraries and utilities ########
cd gmp-4.3.0
./configure --enable-mpfr
make
make check
cd ..
cd mpfr-2.4.1
./configure --with-gmp-build=/home/user/install/gmp-4.3.0
make
make check
cd ..
cd binutils-2.19.1
./configure
make
make DESTDIR=/home/user/gcc install
cd ..
mkdir gcc-4.3.3-bin
cd gcc-4.3.3-bin
../gcc-4.3.3/configure --enable-languages=all --with-gmp-dir=/home/user/install/gmp-4.3.0 --with-mpfr-dir=/home/user/install/mpfr-2.4.1
make bootstrap
mkdir /home/user/gcc
make DESTDIR=/home/user/gcc install
cd ..

######## SET ENVIRONMENT: ########
PATH=/home/user/gcc/usr/local/bin:/home/user/gcc/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.3.3:$PATH
export LIBRARY_PATH=/home/user/gcc/usr/local/lib64:/home/user/gcc/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.3.3
export CPATH=/home/user/gcc/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.3.3/include



And now we're ready to compile CHARMM...

Note that going through the above procedure is not standard requirement for installing CHARMM. Things are a lot easier if the system is moderately up-to-date

Re: testfiles for c35b2 failed
Kenno #21198 06/10/09 10:09 PM
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I'm currently looking for a fix for a problem and I came across this thread, so I'm chipping my two cents worth.

Regarding Lennart's point about user-friendliness my two biggest annoyances with charmm (and I know others share these) are that it's often very difficult to install on todays hardware (c35b2 seems to have solved my pains with opteron installs, but seriously, opterons have been around for ages!!) and the simple fact that the error messages are in most cases "less than useful" The amount of posts I and my collegues have sent to this forum to decipher a cryptic error message and have it turn out to be simple is mind-boggling!

Re: testfiles for c35b2 failed
PhilP #21199 06/10/09 11:01 PM
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I've found most of the 64-bit stuff (esp. for Opteron or EM64T chipsets) has been relatively stable since c33b1, although some of the commercial compilers were not well tested with that version.

The install.com procedure is somewhat arcane, compared to the "configure" and "make" steps for more standard distributed code.

The error messages are generally useful, but some are easily misinterpreted, esp. if one ignores earlier messages in the output.


Rick Venable
computational chemist

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