Turbomole 安装

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INSTALLATION OF TURBOMOLE 6.1

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I) Unpacking

II) Usual installation of Turbomole

III) License file

IV) Testing the binaries on your system(s)

V) Getting started

VI) The parallel version

VII) Problems with parallel version

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Turbomole news, some FAQs, the latest basis sets, documentation, and

tutorial can be found on our web site https://www.360docs.net/doc/e29199658.html,

There is a Turbomole User Mailing List. To subscribe to that list,

just send an email to info@https://www.360docs.net/doc/e29199658.html, with 'subscribe mailing list'

as subject.

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************************************************************************ PLEASE do NOT install Turbomole as root, you would get

problems with read and execute permissions and with the testsuite!!

KERNEL:

The binaries will NOT run on systems with Linux kernel 2.4 any more,

please update your 2.4 systems to kernel 2.6 if you want to run

Turbomole on them.

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I) Unpacking

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1) copy the file(s) turbo*.tar.gz to any directory

(e.g. /local/ or to an NFS or DFS disk)

2) uncompress it/them with gunzip

gunzip *.gz

3) untar it/them

tar -xvf turbo*.tar

this will create a directory TURBOMOLE containing several subdirectories.

4) if you are some kind of a system or Turbomole administrator and if you

are not a member of the same group that has purchased the license,

make sure that the read and execute permissions in scripts/ and bin/* are

set correctly for the right group.

II) Usual installation of Turbomole

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Note: the script Config_turbo_env (and Config_turbo_env.tcsh for csh

users) in the TURBOMOLE directory is doing the configuration if

the variable $TURBODIR has been set. You can set TURBODIR in those

scripts and source the script from your .profile (or .bashrc,

.cshrc, ...).

All users of Turbomole have to declare some shell-variables:

1) The shell-variable TURBODIR has to be set (example for sh/bash/ksh):

export TURBODIR=/local/TURBOMOLE

It has to contain the name of the directory where you have installed Turbomole.

It is recommended to put this line in your .profile (or .bashrc, ...)

2) Check that the script $TURBODIR/scripts/sysname works correctly

on your system:

Call it and make sure that the output consists of just one single line.

Depending on your system it should print out one of these lines:

altix-sgi-linux-gnu # SGI Altix systems (64Bit)

amd64-sun-solaris2 # AMD Opteron system running Solaris (64Bit)

em64t-unknown-linux-gnu # Intel EM64T systems running Linux (64Bit)

i786-pc-linux-gnu # Intel Pentium4/Xeon running Linux (32Bit)

ia64-hp-hpux11 # HP Itanium2 systems running HPUX (64Bit)

ia64-unknown-linux-gnu # Itanium2 systems running Linux (64Bit)

rs6000-ibm-aix5.3 # IBM Power5/Power6 systems running AIX (64Bit) sparc-sun-solaris2 # SUN SPARC systems running Solaris (64Bit)

x86_64-unknown-linux-gnu # AMD Opteron systems running Linux (64Bit) winnt # generic Windows32 binaries (32Bit)

i686-apple-darwin9 # Mac OS X for Intel CPUs (64bit) Most of the Turbomole scripts like jobex or TEST do need a correct

sysname output. You will get strange errors if this is not the case!

3) Finally you have to set the PA TH's (bash/ksh syntax):

export PA TH=$TURBODIR/scripts:$PA TH

export PA TH=$TURBODIR/bin/`sysname`:$PA TH

Put this in your .profile (.bashrc,...) if you want to do calculations.

III) License file

To get a valid license file for Turbomole 6.1, the program

$TURBODIR/LICENSE/get_node_info

has to be executed on each node that shall be used for Turbomole

calculations.

Send the output of all those runs to your local reseller or to COSMOlogic.

The output data is needed to generate a license file called

turbo_license.ctd

which you have to copy to $TURBODIR/LICENSE as soon as you have received it.

IV) Testing the binaries on your system(s)

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To test Turbomole with the Testsuite, use the shell-script TTEST.

Change-dir to $TURBODIR/TURBOTEST and then call TTEST

If the tests fail, please check your read-write permissions in

$TURBODIR/TURBOTEST. If your problem is not solved by the FAQ (see https://www.360docs.net/doc/e29199658.html,), please write an email to turbomole@cosmologic.de

SGI Altix and IBM systems:

The binaries on SGI Altix and IBM systems are dynamically linked.

If Turbomole fails to run, please call

ldd $TURBODIR/bin/`sysname -s`/ridft

and check if there are any unresolved libraries.

Please ask your system administrator to install missing libraries!

V) Getting started

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See chapter 1 of the documentation (in $TURBODIR/DOK) how to use Turbomole, and read the tutorial (also in $TURBODIR/DOK).

Please run the Testsuite before you start your own calculations.

VI) The parallel version

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The parallel version of Turbomole is MPI based and uses

1.) HP MPI , see https://www.360docs.net/doc/e29199658.html,/go/mpi

2.) on all other Unix systems (IBM, HP, SGI, DEC, SUN,...)

the MPI library that was shipped with your operating system.

USING THE PARALLEL VERSION:

- set PARA_ARCH to MPI (sh/bash-syntax:)

export PARA_ARCH=MPI

sysname will now append '_mpi' to its output

- HP-MPI does not need to be installed on your system, all scripts and functionality comes with the Turbomole distribution.

HP-MPI uses by default the fastest interconnect that it finds on

your system: Shared Memory, Infiniband, Myrinet, TCP/IP

- HP-MPI does not need to be licensed. COSMOlogic and HP made an agreement that allows all Turbomole users the free usage of HP-MPI

- non-Linux systems:

check that mpirun is in your $PATH and that your MPI-environment runs without problems (it is called poe on IBM AIX machines or mprun under Solaris)

- if you want to call the parallel ridft, rdgrad, dscf, grad, ricc2, ormpgrad from your shell, you have to extend the PATH (sh/bash syntax):

export PA TH=$TURBODIR/bin/`sysname`:$PA TH

this is not necessary if you're just using jobex or TTEST

- set the Number of CPU's that should be used with the variable PARNODES

export PARNODES=2

(default is 2)

NOTE: all parallel Turbomole programs except ricc2 need an additional server task which is not doing any calculations. The server will be

started automatically, but there will be $PARNODES+1 tasks running

on your system. This is important if you're going to use a

queueing system. The scripts in Turbomole will automatically add

an additional node to list of machines, so you will just have

to request as many CPUs from the queuing system as you have set in $PARNODES

- you can TTEST the parallel version with the Testsuite.

Just go to $TURBODIR/TURBOTEST and call 'TTEST'

BUT NOTE: some tests will only pass if not more than 2 CPUs are used!

Therefore the tests will only be performed for

$PARNODES=2

To run single tests also on more CPUs, change the last option in the $TURBODIR/TURBOTEST/DEFCRIT file, but

be aware that not all tests will pass!

- parallelTurbomole is prepared for running under the queueing systems DQS, PBS and IBM's loadleveler, it should also run with LSF and SGE queuing systems.

If you are not starting the parallel binaries from a queuing system,

all clients will be started on the local node. To use your own list

of machines that should be used for the calculation, create a file with

that list (one machine name per line) and set the environment variable HOSTS_FILE to that file.

VII) Problems with parallel version

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HP-MPI:

If the parallel calculations fail and if you find a message in the output like:

mpid: Cannot create shared memory segment

then the default amount of shared memory allocated for all processes is too small. This amount can be set by changing the environment variable MPI_GLOBMEMSIZE=

to a reasonable number, number is given in Byte.

General:

The stack size limit has to be set to unlimited or at least to a reasonable size. This can be done at the command line in the serial version with: ulimit -s unlimited

for bash/sh/ksh users or

limitstacksize unlimited

forcsh/tcsh users.

However, this is not sufficient when using rsh/ssh on a cluster. On all nodes, /etc/security/limits.conf has to be modified and a line

* soft stack 4194303

must be added.