Subject: RE: Gaussian calculation speed

From: "Jason L. Douglas" <[email-masked]>
Date: Wed, 31 Oct 2001 00:33:39 -0500

I would imagine the I/O subsystem to be a serious determining performance
factor with SCF calculations, unless you're doing direct SCF. I've had
similar results between a Dell PIII 450 with a SCSI disk, and a Dell PIII
733 with ATA. I understand that with Linux systems, I/O speed can vary
greatly on how you've setup the OS, but I'm not intimately familiar with Red
Hat 6 or 7, so I can't offer any real suggestions there. I'm sure if you
replaced the ATA drive with a single SCSI drive, or even a SCSI RAID array,
coupled with a good SCSI adapter, you'd have a very fast system, utilizing
more of the faster processing speed. Hope that helps!

Jason Douglas

---

From: Jochen Buehler <[email-masked]>
Date: Wed, 31 Oct 2001 09:37:18 +0100 (CET)

Elena Jakubikova writes:
 > Dear CCLers,
 > 
 > I have run one CISD calculation with a relatively large
 > basis set on CH4 molecule on 2 different computers.
 > Computer one is Dell 550MHz Pentium III, 512MB RAM
 > (100MHz SDRAM), 18 GB SCSI #1 Hard Drive, and Red Hat
 > Linux 6.0 operating system. Computer two is Millennia
 > 733MHz Pentium III, 770MB RAM (133MHz SDRAM), 27GB IDE
 > ATA-66 hard drive, and Red Hat Linux 7.0 operating
 > system.
 > To my big surprise the calculation was much faster on
 > Dell (job cpu time = 24 minutes 1.8 sec) than on
 > Millennia (job cpu time = 1 hour 4 minutes 18.6
 > seconds). 

Seems like you are using PIO transfer mode on Millenia.
What does the output of hdparm say?
Because of the disk I/O required for the job the (always operating 
in DMA mode) SCSI system is faster.

Regards,

Jochen

--
Jochen Buehler, Dipl.-Chem      EMail:  [email-masked]
AG Prof. Dr. Daltrozzo                 [email-masked]
Fachbereich Chemie              Phone: +49-7531-882095
Universitaet Konstanz           Fax:   +49-7531-883043
78457 Konstanz, Germany

---

From: Toomas Tamm <[email-masked]>
Date: Wed, 31 Oct 2001 09:47:28 +0200

> more of the faster processing speed. Hope that helps!

Indeed, several distributions of Linux do not turn on the ATA-66 (or
ATA-100) support by default. One can make a quick test of disk speed
(as root) with "hdparm -t /dev/hda"  (or /dev/sda for SCSI). Results
in 4-5 MB/sec range indicate that the ATA support is off. A modern
disk should deliver around 20-30 MB/sec with ATA-66 or ATA-100.

For serious benchmarking, a more advanced tool, e.g. "bonnie" is
recommended. 

One can enable UDMA (ATA-66 / ATA-100) on IDE disks with "hdparm -d1
/dev/hda" or similar. Other flags such as -c1 or -m16 to hdparm may
benefit as well, but may also lead to data loss, so proceed very
carefully. Avoid the -X flag to hdparm: I have personally had a case
of data loss with such setup.

-- 
Toomas Tamm                                 e-mail: [email-masked]
Inorganic and General Chemistry             voice:  INT+372-620-2810
Tallinn Technical University                fax:    INT+372-620-2796
Ehitajate tee 5, EE-19086 Tallinn, Estonia  http://www.kk.ttu.ee/toomas/

---

From: Lars Packschies <[email-masked]>
Date: Wed, 31 Oct 2001 10:03:52 +0100

> Hat 6 or 7, so I can't offer any real suggestions there. I'm sure if you

Dear Elena,

Jason suggested that it may be the I/O-Subsystem. If it's the case it
can be tuned: 

When you type (as superuser)

  hdparm -tT /dev/hda          (or whatever the device of the HD is)

you should get something like

/dev/hda:
 Timing buffer-cache reads:   128 MB in  1.26 seconds =101.59 MB/sec
 Timing buffered disk reads:  64 MB in  3.56 seconds = 17.98 MB/sec

if your HD is set up using the correct DMA and PIO modes.

If not, you get values like

30 MB/sec (buffer-cache reads) and
3  MB/sec (buffered disk reads)

for example. The values above show the HD in my RH 7 System, and its not
one of the fastest.

To set up the drive with hdparm look at the options with hdparm -h. And
be careful. I just switched on DMA and 32-bit I/O-Support.

hdparm /dev/hda shows you how the HD is configured.

"Newer" 2.4 kernels (and late 2.2? not sure) can be set up to use DMA if
available (I think it is the default setting). If you have an older
kernel that does not support 32 bit I/O-Support you should get a new
one. 

Good luck,

Lars

---

From: Serguei Patchkovskii <[email-masked]>
Date: Wed, 31 Oct 2001 08:55:12 -0500

On Tue, 30 Oct 2001, Elena Jakubikova wrote:
> I tried to run top while running only this one
> calculation and found out that during the extensive I/O
> phase of calculation (l804,l913), there is a lot of CPU
> used by the system on Millennia computer (at certain
> moments its more than 90%), whereas in the case of Dell
> computer almost all cpu is used by the user.

Most likely, running:

/sbin/hdparm -d 1 /dev/hdc # Or whatever your scratch disk 
                           # device is

will improve results. You need to run this command as root,
so ask your system administrator to do it for you (and to
add the command to an appropriate startup file).

To check how much difference it makes for I/O transfers, run

/dev/hdparm -t /dev/hdc # Again, whatever your scratch disk is

before and after turning on DMA. It is not uncommon to see
an order of magnitude improvement in transfer speed, once 
DMA is turned on.

Regards,

Dr. Serguei Patchkovskii

Tel: +1-(613)-991-2719
Fax: +1-(613)-947-2838
E-mail: [email-masked]

Research Council Officer
Steacie Institute for Molecular Sciences
National Research Council Canada
Room 2158, 100 Sussex Drive
Ottawa, Ontario
K1A 0R6 Canada

---

From: Mikael Johansson <[email-masked]>
Date: Wed, 31 Oct 2001 18:04:26 +0200 (EET)

Hello All!

Our traditional series of Winter Schools in Theoretical Chemistry
continues. See http://www.chem.helsinki.fi/Info/WinterSchool/

The topic of this year's school is CONDENSED PHASE DYNAMICS.

Please register as soon as possible. The program is enclosed. It is also
available on the web-site, where eventual changes will appear.

Have a nice day,
    Mikael Johansson
    University of Helsinki
    Department of Chemistry
    [email-masked]
    Phone: +358-9-191 50185
    FAX  : +358-9-191 50169

*****************************************************************
****                                                         ****
****       Winter School in Theoretical Chemistry 2001       ****
****                                                         ****
****                CONDENSED PHASE DYNAMICS                 ****
****                                                         ****
*****************************************************************

  TIME:       10-13 December, 2001. (Start at 10:00 on Monday)

  VENUE:      Department of Chemistry, University of Helsinki,
              A.I. Virtasen aukio 1, Helsinki, Finland.

  LANGUAGE:   English.

  LECTURERS:  Dominik Marx (4 h) (Bochum):
              "Ab initio molecular dynamics: theory I,II"
              "Ab initio molecular dynamics: applications I,II"

              Alexander Nemukhin (5 h) (Moscow): "Construction of
              potential energy surfaces for modelling structure, spectra
              and dynamics in condensed phases with emphasis on DIM
              (Diatomics in Molecules)"

              Risto Nieminen (2h) (Espoo): "Linear and nonlinear response
              using time-dependent density-functional theory,"
              "Multiscale modelling of anisotropic chemical etching"

              Kai Nordlund (2h) (Helsinki): Mechanism of bond-breaking
              induced erosion of amorphous hydrogenated carbon, with
              application to fusion reactors", "Recrystallization
              mechanism of semiconductors by electron-irradiation-induced
              bond breaking"

              Burkhard Schmidt (4h) (Berlin): "Condensed phase dynamics;
              quantum dynamics, quantum-classical methods (trajectories,
              Gauss-packets, surface-hopping, photodissociation)"

  PROGRAM: (version 1.0)

                 Monday                Tuesday               Wednesday

  09:15-10:00                          Marx I                Schmidt IV
  10:00-10:30    Welcome               Break                 Break
  10:30-11:15    Nemukhin I            Marx II               Nieminen II
  11:30-12:15    Nemukhin II           Nemukhin III          Marx III
  12:15-13:30    Lunch & posters       Lunch & posters       Lunch & posters
  13:30-14:15    Schmidt I             Nemukhin IV           Marx IV
  14:15-14:45    Break                 Break                 Break
  14:45-15:30    Schmidt II            Schmidt III           Nemukhin V
  15:45-16:30    Nordlund I            Nieminen I            Nordlund II
  16:30-         Posters               Comp. Chem.           Departure
                                       Section Meeting

  Tuesday 16.30: Meeting of the Computational Chemistry Section in the
                 Laboratory of Instruction in Swedish.

  CONTRIBUTED    Any member of the School is welcome to put up
  PAPERS:        a poster on the premises.

  PROCEEDINGS:   None.

  LEVEL:         Post-graduate and research, for scientists already
                 involved in computational quantum chemistry. The course
                 is obligatory for PhD-students within the LASKEMO grad
                 school. This year the exam will be replaced by an essay.
                 The course will give 2 credits.

  FEES:          University students and staff: none.

  ADMISSION:     The participants are requested to register
                 by 15 November, 2001 to the address below.
                 Note that MOLPROP members should contact Dage.

                 Dr Juha Vaara, Department of Chemistry,
                 P.O.Box 55 (A.I. Virtasen aukio 1),
                 FIN-00014 University of Helsinki, Finland.
                 Telephone: 358-9-191 50181.
                 FAX:       358-9-191 50169.

                 E-mail: [email-masked]

  MOLPROP        Dr Dage Sundholm, Department of Chemistry,
                 P.O.Box 55 (A.I. Virtasen aukio 1),
                 FIN-00014 University of Helsinki, Finland
                 Telephone: 358-9-19150 176
                 FAX:       358-9-19150 169

                 Email: [email-masked]

---

From: Bernd Schubert <[email-masked]>
Date: Wed, 31 Oct 2001 17:16:39 +0100

> of data loss with such setup.

But without the -X flag you only enable to use dma-1 --> with a maximum 
transferrate of 16 MB/s. Using the -X flag you enable Ultra-DMA (ATA-33 -- 
-X34, ATA-66 -- -X66, etc.).

Bernd