Atlas library, SL7, libf77?

[Nathan Moore]

For a colleague, I am installing gamess on a cluster of SL7 machines.  As
an initial effort, compiling with gfortran, atlas libraries and sockets for
message passing.  Compiling is successful, but at the linking stages,
gamess can't find the lf77blas library.

I can't find lf77blas either (in the yum repo), but it seems like it is at
least sometimes included in atlas.  Is there a standard place that this
library is availble?

from gamess,



[root@pilgrim gamess]# ./lked gamess 01

Thu Dec 17 10:42:35 CST 2015

GAMESS will be linked into the binary file gamess.01.x.



The name of the linker on this machine is gfortran,

and the linker options are " ".



Object code list begins "gamess.o unport.o",

followed by   BLAS object code " ",

followed by LAPACK object code "dgeev.o dgesvd.o zheev.o",

followed by VECTOR object code " ",

followed by memory object code "zunix.o",

followed by the standard GAMESS object code list,


...


   The message passing libraries searched are

/opt/gamess/ddi/libddi.a -lpthread



   Other libraries, including math libraries, to be searched are

-L/usr/lib64/atlas -lf77blas -latlas



Linker messages (if any) follow...

/usr/bin/ld: cannot find -lf77blas

collect2: error: ld returned 1 exit status


and yum says,

[root@pilgrim gamess]# yum list | grep atlas

atlas.x86_64 3.10.1-7.el7   @sl

atlas-devel.x86_64   3.10.1-7.el7   @sl

atlas-sse2.i686  3.10.1-7.el7   @sl

atlas-sse3.i686  3.10.1-7.el7   @sl

atlas-static.x86_64  3.10.1-7.el7   @sl

atlas.i686   3.10.1-7.el7   sl

atlas-devel.i686 3.10.1-7.el7   sl

atlas-static.i6863.10.1-7.el7   sl


but, the libf77blas isn't there,

[root@pilgrim gamess]# ls /usr/lib64/atlas/

libatlas.alibsatlas.so.3 libtatlas.solibtatlas.so.3.10

libsatlas.so  libsatlas.so.3.10  libtatlas.so.3

[root@pilgrim gamess]# ls /usr/lib/atlas-sse2/

libsatlas.so.3  libsatlas.so.3.10  libtatlas.so.3  libtatlas.so.3.10

[root@pilgrim gamess]# ls /usr/lib/atlas-sse3/

libsatlas.so.3  libsatlas.so.3.10  libtatlas.so.3  libtatlas.so.3.10


​I suppose I'll build my own - was wondering though if there's a yum
package I'm missing.

Nathan​

-- 
- - - - - - -   - - - - - - -   - - - - - - -
Nathan Moore
Mississippi River and 44th Parallel
- - - - - - -   - - - - - - -   - - - - - - -

Re: Security ERRATA Critical: firefox on SL5.x, SL6.x i386/x86_64

[Clint Bowman]

Connie,

What's this "(7363)/ 
KStartupInfo::createNewStartupId:" that I'm seeing with this morning's 
update?


Message appeared twice in the "Updating" portion following:

Updating   : selinux-policy-3.7.19-279.el6_7.8.noarch
and
Updating   : filezilla-3.7.3-3.el6.x86_64

and once in the "Installing" section following

kernel-devel-2.6.32-573.12.1.el6.x86_64

Also appeared twice in the "Cleanup" section following:

 Cleanup: x2goagent-3.5.0.32-2.el6.x86_64
and
Cleanup: kernel-headers-2.6.32-573.3.1.el6.x86_64

I fail to see any pattern that would lead me to understanding.

yum.log does not have any complaints.

TIA

Clint

Clint BowmanINTERNET:   cl...@ecy.wa.gov
Air Quality Modeler INTERNET:   cl...@math.utah.edu
Department of Ecology   VOICE:  (360) 407-6815
PO Box 47600FAX:(360) 407-7534
Olympia, WA 98504-7600

USPS:   PO Box 47600, Olympia, WA 98504-7600
Parcels:300 Desmond Drive, Lacey, WA 98503-1274

On Thu, 17 Dec 2015, Connie Sieh wrote:


Synopsis:  Critical: firefox security update
Advisory ID:   SLSA-2015:2657-1
Issue Date:2015-12-16
CVE Numbers:   CVE-2015-7201
  CVE-2015-7210
  CVE-2015-7212
  CVE-2015-7205
  CVE-2015-7213
  CVE-2015-7222
  CVE-2015-7214
--

Several flaws were found in the processing of malformed web content. A web
page containing malicious content could cause Firefox to crash or,
potentially, execute arbitrary code with the privileges of the user
running Firefox. (CVE-2015-7201, CVE-2015-7205, CVE-2015-7210,
CVE-2015-7212, CVE-2015-7213, CVE-2015-7222)

A flaw was found in the way Firefox handled content using the 'data:' and
'view-source:' URIs. An attacker could use this flaw to bypass the same-
origin policy and read data from cross-site URLs and local files.
(CVE-2015-7214)

5.0 ESR, which corrects these issues. After installing the update, Firefox
must be restarted for the changes to take effect.
--

SL5
 x86_64
   firefox-38.5.0-2.el5_11.i386.rpm
   firefox-38.5.0-2.el5_11.x86_64.rpm
   firefox-debuginfo-38.5.0-2.el5_11.i386.rpm
   firefox-debuginfo-38.5.0-2.el5_11.x86_64.rpm
 i386
   firefox-38.5.0-2.el5_11.i386.rpm
   firefox-debuginfo-38.5.0-2.el5_11.i386.rpm
SL6
 x86_64
   firefox-38.5.0-2.el6_7.x86_64.rpm
   firefox-debuginfo-38.5.0-2.el6_7.x86_64.rpm
   firefox-38.5.0-2.el6_7.i686.rpm
   firefox-debuginfo-38.5.0-2.el6_7.i686.rpm
 i386
   firefox-38.5.0-2.el6_7.i686.rpm
   firefox-debuginfo-38.5.0-2.el6_7.i686.rpm


- Scientific Linux Development Team

Re: some naive question from new user

[Connie Sieh]

On Sun, 13 Dec 2015, Albert wrote:


Dear:

I am a new Scientific user and I've got some naive questions. I would be
appreciated if somebody can give me some advice.

(1) I found there are different iso file from:

http://ftp1.scientificlinux.org/linux/scientific/7x/x86_64/iso/

If I would like to install X64 plus 32 bit environment libraries, which
one should I download? I am going to do some professional computational
work under Scientific Linux, and many software may need various
libraries such as: python, libsqt, libstdc, gcc, boost, perl and so on.


Either of the DVD ones.



Would the following iso be sufficient for my purpuse?

SL-7-Everything-Dual-Layer-DVD-x86_64-2015-04-07-7.1.iso 06-Apr-2015
11:376.6G


Yes but as the name suggests you need to burn to a dual layer DVD.



(2) How can we install the 32bit library? I rember there is no any
options of selecting 32bit library during the first refreshing
installing Redhat. I don't know what's the situation of SL-7..


Same for SL 7.



(3) If some library is missing from above DVD file, where can I can
something additonal? How can we add local iso to software repository?
How can we add a online address to software repository?


You can use YUM to install packages after the initial install via online 
access as this is available by default.


Adding ISO as a software repository would require that you make a 
"something.repo" file in /etc/yum.repos.d/  .  Look at existing ones for a 
example of what to do.




(4) Recently I bough a very new laptop  HP pavilion SE 15 and the Wlan
is intel dual band wireless ac 3165. I am just wondering, will SL-7
support WIFI in the laptop?


I suspect so as Intel is fairly well supported.



Thank you very much

Albert



--
--

Connie J. Sieh
Computing Services Specialist III

Fermi National Accelerator Laboratory
630 840 8531 office

http://www.fnal.gov
cs...@fnal.gov

Re: Atlas library, SL7, libf77?

[Nathan Moore]

Here's an interesting feature I discovered while compiling the Atlas
library. During the compilation the Makefile tests out a number of
different, let's call them, block sizes, which are used in the matrix
multiplication routines.

I get The mpression that the developers believe that the test for what
block size is optimal will be affected by the CPU speed , so, the configure
command that you run before make will flat out refuse to finish if you have
the standard cool and quiet, or whatever it's called in Intel world, CPU
frequency scaling running.

The workaround is to reboot your machine , go into the BIOS , turn off the
frequency scaling, and then configure; make ; make install. This was a
little surprising to discover, it's not often that a software packages
forces you to make good life choices. Normally it seems like gentle
suggestions are the default.
On Dec 17, 2015 11:18 AM, "Nathan Moore"  wrote:

> For a colleague, I am installing gamess on a cluster of SL7 machines.  As
> an initial effort, compiling with gfortran, atlas libraries and sockets for
> message passing.  Compiling is successful, but at the linking stages,
> gamess can't find the lf77blas library.
>
> I can't find lf77blas either (in the yum repo), but it seems like it is at
> least sometimes included in atlas.  Is there a standard place that this
> library is availble?
>
> from gamess,
>
>
>
> [root@pilgrim gamess]# ./lked gamess 01
>
> Thu Dec 17 10:42:35 CST 2015
>
> GAMESS will be linked into the binary file gamess.01.x.
>
>
>
> The name of the linker on this machine is gfortran,
>
> and the linker options are " ".
>
>
>
> Object code list begins "gamess.o unport.o",
>
> followed by   BLAS object code " ",
>
> followed by LAPACK object code "dgeev.o dgesvd.o zheev.o",
>
> followed by VECTOR object code " ",
>
> followed by memory object code "zunix.o",
>
> followed by the standard GAMESS object code list,
>
>
> ...
>
>
>The message passing libraries searched are
>
> /opt/gamess/ddi/libddi.a -lpthread
>
>
>
>Other libraries, including math libraries, to be searched are
>
> -L/usr/lib64/atlas -lf77blas -latlas
>
>
>
> Linker messages (if any) follow...
>
> /usr/bin/ld: cannot find -lf77blas
>
> collect2: error: ld returned 1 exit status
>
>
> and yum says,
>
> [root@pilgrim gamess]# yum list | grep atlas
>
> atlas.x86_64 3.10.1-7.el7   @sl
>
> atlas-devel.x86_64   3.10.1-7.el7   @sl
>
> atlas-sse2.i686  3.10.1-7.el7   @sl
>
> atlas-sse3.i686  3.10.1-7.el7   @sl
>
> atlas-static.x86_64  3.10.1-7.el7   @sl
>
> atlas.i686   3.10.1-7.el7   sl
>
> atlas-devel.i686 3.10.1-7.el7   sl
>
> atlas-static.i6863.10.1-7.el7   sl
>
>
> but, the libf77blas isn't there,
>
> [root@pilgrim gamess]# ls /usr/lib64/atlas/
>
> libatlas.alibsatlas.so.3 libtatlas.solibtatlas.so.3.10
>
> libsatlas.so  libsatlas.so.3.10  libtatlas.so.3
>
> [root@pilgrim gamess]# ls /usr/lib/atlas-sse2/
>
> libsatlas.so.3  libsatlas.so.3.10  libtatlas.so.3  libtatlas.so.3.10
>
> [root@pilgrim gamess]# ls /usr/lib/atlas-sse3/
>
> libsatlas.so.3  libsatlas.so.3.10  libtatlas.so.3  libtatlas.so.3.10
>
>
> ​I suppose I'll build my own - was wondering though if there's a yum
> package I'm missing.
>
> Nathan​
>
> --
> - - - - - - -   - - - - - - -   - - - - - - -
> Nathan Moore
> Mississippi River and 44th Parallel
> - - - - - - -   - - - - - - -   - - - - - - -
>
>