i have set variable LD_FLAGS = static in make.sys file <br><br>and on $make all<br><br>i get error<br>----------------------------------------<br>libiotk.a<br>mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c iotk_print_kinds.f90<br>
make loclib_only<br>make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src'<br>make[3]: Nothing to be done for `loclib_only'.<br>make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src'<br>
mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a <br>/opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open':<br>(.text+0x123): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking<br>
/opt/openmpi/lib/libopen-rte.a(sys_info.o): In function `orte_sys_info':<br>(.text+0x16f): warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking<br>
/opt/openmpi/lib/libopen-pal.a(if.o): In function `opal_ifaddrtoname':<br>(.text+0x780): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `__malloc_check_init':<br>(.text+0x1060): multiple definition of `__malloc_check_init'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first defined here<br>
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 144 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_free':<br>
(.text+0x2230): multiple definition of `_int_free'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first defined here<br>/usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_malloc':<br>(.text+0x2a50): multiple definition of `_int_malloc'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first defined here<br>
/usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 3916 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_memalign':<br>
(.text+0x3900): multiple definition of `_int_memalign'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first defined here<br>/usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 577 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_valloc':<br>(.text+0x3c30): multiple definition of `_int_valloc'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first defined here<br>
/usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 378 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_realloc':<br>
(.text+0x3d80): multiple definition of `_int_realloc'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first defined here<br>/usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 875 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `free':<br>(.text+0x5f20): multiple definition of `free'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first defined here<br>
/usr/bin/ld: Warning: size of symbol `free' changed from 256 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `malloc':<br>
(.text+0x4690): multiple definition of `malloc'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first defined here<br>/usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `realloc':<br>(.text+0x60f0): multiple definition of `realloc'<br>/opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first defined here<br>
/usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>collect2: ld returned 1 exit status<br>
make[2]: *** [iotk_print_kinds.x] Error 1<br>make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src'<br>make[1]: *** [lib+util] Error 2<br>make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk'<br>
make: *** [libiotk] Error 2<br><br>---------------------------------------------<br><br>sincerely<br><br><br><div class="gmail_quote">On Sun, Sep 6, 2009 at 11:35 PM, <span dir="ltr"><<a href="mailto:pw_forum-request@pwscf.org">pw_forum-request@pwscf.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: pw.x running but nothing happens (Bipul Rakshit)<br>
2. pseudo potential (Mansoureh Pashangpour)<br>
3. Re: error loading shared libraries on parallel execution<br>
(Paolo Giannozzi)<br>
4. Re: pw.x running but nothing happens (Lorenzo Paulatto)<br>
5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 6 Sep 2009 08:03:29 +0100<br>
From: Bipul Rakshit <<a href="mailto:bipulrr@gmail.com">bipulrr@gmail.com</a>><br>
Subject: Re: [Pw_forum] pw.x running but nothing happens<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:3a749910909060003k38e7f62fn4aa040900b71b42c@mail.gmail.com">3a749910909060003k38e7f62fn4aa040900b71b42c@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="gb2312"<br>
<br>
Dear Wangqj,<br>
The same thing happens to me.<br>
since you are using large no. of wfc, although it shows the job is running<br>
in 8 procs, but sometimes if the installation is not proper, it is running<br>
in 1 procs only.<br>
<br>
So better you check the parallel installation using a small job, with<br>
different no. of procs and see whether its taking lesser time as no. of<br>
procs increases or not?<br>
<br>
cheers<br>
<br>
2009/9/6 wangqj1 <<a href="mailto:wangqj1@126.com">wangqj1@126.com</a>><br>
<br>
><br>
> Dear pwscf users<br>
> When I run vc-relax on the computing cluster use one node which has 8<br>
> CPUs.<br>
> The output file is as following:<br>
><br>
> Program PWSCF v.4.0.1 starts ...<br>
> Today is 6Sep2009 at 7:49:30<br>
> Parallel version (MPI)<br>
> Number of processors in use: 8<br>
> R & G space division: proc/pool = 8<br>
> For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW<br>
> .....................................................................<br>
> Initial potential from superposition of free atoms<br>
> starting charge 435.99565, renormalised to 436.00000<br>
> Starting wfc are 254 atomic + 8 random wfc<br>
><br>
> After one day ,it still like this and no iteration has completed ,there is<br>
> also no error was turn up .There is no error in the input file because I<br>
> have test it on anthoer computer which has 4 CPUs and it runs well .<br>
> I can't find the reason about this ,any help will be appreciated .<br>
> Best Regards<br>
> Q.J.Wang<br>
> XiangTan University<br>
><br>
><br>
><br>
> ------------------------------<br>
> ???????????,<a href="http://www.yeah.net" target="_blank">www.yeah.net</a> <<a href="http://www.yeah.net/?from=footer" target="_blank">http://www.yeah.net/?from=footer</a>><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
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><br>
><br>
<br>
<br>
--<br>
Dr. Bipul Rakshit<br>
Research Associate,<br>
S N Bose Centre for Basic Sciences,<br>
Salt Lake,<br>
Kolkata 700 098<br>
India<br>
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Message: 2<br>
Date: Sun, 6 Sep 2009 11:25:06 +0330<br>
From: Mansoureh Pashangpour <<a href="mailto:mansourehp@gmail.com">mansourehp@gmail.com</a>><br>
Subject: [Pw_forum] pseudo potential<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:cbe1626b0909060055o66690789yc0ae02efdfa5391e@mail.gmail.com">cbe1626b0909060055o66690789yc0ae02efdfa5391e@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear all<br>
how can I plot these pseudo potentials? how can I discribe the properties<br>
of pseudo potentials?<br>
<br>
*Fe.pbe-nd-rrkjus.UPF*<<a href="http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF" target="_blank">http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF</a>><br>
(<br>
*details*<<a href="http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF" target="_blank">http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF</a>>)<br>
<br>
<br>
Perdew-Burke-Ernzerhof (PBE) exch-corr<br>
nonlinear core-correction<br>
semicore state d in valence<br>
Rabe Rappe Kaxiras Joannopoulos (ultrasoft)<br>
<br>
and<br>
<br>
*H.pbe-rrkjus.UPF* <<a href="http://www.pwscf.org/pseudo/1.3/UPF/H.pbe-rrkjus.UPF" target="_blank">http://www.pwscf.org/pseudo/1.3/UPF/H.pbe-rrkjus.UPF</a>><br>
(*details* <<a href="http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF" target="_blank">http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF</a>>)<br>
<br>
<br>
Perdew-Burke-Ernzerhof (PBE) exch-corr<br>
Rabe Rappe Kaxiras Joannopoulos (ultrasoft)<br>
<br>
<br>
and<br>
<br>
*O.pbe-rrkjus.UPF*<br>
<<a href="http://www.pwscf.org/pseudo/1.3/UPF/O.pbe-rrkjus.UPF" target="_blank">http://www.pwscf.org/pseudo/1.3/UPF/O.pbe-rrkjus.UPF</a>> (*details*<br>
<<a href="http://www.pwscf.org/pseudo/upfdetails.php?upf=O.pbe-rrkjus.UPF" target="_blank">http://www.pwscf.org/pseudo/upfdetails.php?upf=O.pbe-rrkjus.UPF</a>>)<br>
<br>
Perdew-Burke-Ernzerhof (PBE) exch-corr<br>
Rabe Rappe Kaxiras Joannopoulos (ultrasoft)<br>
<br>
<br>
Thanks<br>
Mansoureh Pashangpour<br>
Ph.D student<br>
Islami Azad university<br>
science & reaserch branch<br>
Tehran, IRAN<br>
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Message: 3<br>
Date: Sun, 6 Sep 2009 10:24:48 +0200<br>
From: Paolo Giannozzi <<a href="mailto:giannozz@democritos.it">giannozz@democritos.it</a>><br>
Subject: Re: [Pw_forum] error loading shared libraries on parallel<br>
execution<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:E6918F77-0C97-4F26-9F7E-BE790E9EFC6B@democritos.it">E6918F77-0C97-4F26-9F7E-BE790E9EFC6B@democritos.it</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed<br>
<br>
<br>
On Sep 6, 2009, at 1:20 , sreekar guddeti wrote:<br>
<br>
> plz suggest solutions which donot require root permissions ,<br>
> as i dont have<br>
<br>
somebody must have it. Report the problem and the<br>
solution (i.e. install gfortran on ALL processors) to<br>
whoever has root access. As an alternative, try static<br>
link (add -static to LDFLAGS in make.sys).<br>
---<br>
Paolo Giannozzi, Dept of Physics, University of Udine<br>
via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST)<br>
From: "Lorenzo Paulatto" <<a href="mailto:paulatto@sissa.it">paulatto@sissa.it</a>><br>
Subject: Re: [Pw_forum] pw.x running but nothing happens<br>
To: "PWSCF Forum" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:46134.78.12.159.112.1252232440.squirrel@webmail.sissa.it">46134.78.12.159.112.1252232440.squirrel@webmail.sissa.it</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
<br>
On Sun, September 6, 2009 02:33, wangqj1 wrote:<br>
> After one day ,it still like this and no iteration has completed ,there<br>
> is<br>
> also no error was turn up .There is no error in the input file because I<br>
> have test it on anthoer computer which has 4 CPUs and it runs well .<br>
> I can't find the reason about this ,any help will be appreciated .<br>
<br>
<br>
Dear QJ,<br>
this is strange. But we would need more information on your hardwre<br>
configuration in order to help you. In the mean while you can check the<br>
behaviour of te pw.x processes with "top". E.g. if they are all runing at<br>
100% CPU, how much memory they are taking and so on.<br>
<br>
regards<br>
<br>
<br>
--<br>
Lorenzo Paulatto<br>
SISSA & DEMOCRITOS (Trieste)<br>
phone: +39 040 3787 511<br>
skype: paulatz<br>
www: <a href="http://people.sissa.it/%7Epaulatto/" target="_blank">http://people.sissa.it/~paulatto/</a><br>
<br>
<br>
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------------------------------<br>
<br>
Message: 5<br>
Date: Sun, 6 Sep 2009 23:35:26 +0530<br>
From: sreekar guddeti <<a href="mailto:colonel.sreekar@gmail.com">colonel.sreekar@gmail.com</a>><br>
Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:c864e4460909061105i43b1885dh6141b2789b8ae51@mail.gmail.com">c864e4460909061105i43b1885dh6141b2789b8ae51@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
@duy lee<br>
i inserted the line #$ -V in my qsub script and the env variable<br>
$LD_LIBRARY_PATH is being set from script... thanks for that but still<br>
problem persists.<br>
<br>
@rakshit<br>
<br>
-----------------------------<br>
$find /usr/lib -name libgfortran*<br>
-----------------------------<br>
and output is<br>
_______________________<br>
/usr/lib/libgfortran.so.1.0.0<br>
/usr/lib/libgfortran.so.1<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a<br>
/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so<br>
_______________________<br>
whereas on doing<br>
-----------------------------<br>
$find /usr/lib64 -name libgfortran*<br>
-----------------------------<br>
ouput is<br>
_________________<br>
/usr/lib64/libgfortran.so.3.0.0<br>
/usr/lib64/libgfortran.so.1.0.0<br>
/usr/lib64/libgfortran.so.1<br>
find: /usr/lib64/audit: Permission denied<br>
*/usr/lib64/libgfortran.so.3*<br>
_________________<br>
<br>
it means my OS has the required library, i guess<br>
<br>
i installed the QE on the head node<br>
This cluster is a Rocks cluster with<br>
<br>
# of nodes: 10 (1 head node + 9 compute nodes)<br>
# of processors/node: 8<br>
# Total # of processors: 10X8 = 80<br>
<br>
i tested the sample program for submitting batch jobs using SGE utility and<br>
it is working fine(<br>
<a href="http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html" target="_blank">http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html</a>)<br>
<br>
sincerely,<br>
sreekar guddeti<br>
Dept. Physics<br>
IIT Bombay<br>
India<br>
<br>
<br>
On Sun, Sep 6, 2009 at 12:28 PM, <<a href="mailto:pw_forum-request@pwscf.org">pw_forum-request@pwscf.org</a>> wrote:<br>
<br>
> Send Pw_forum mailing list submissions to<br>
> <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
><br>
> To subscribe or unsubscribe via the World Wide Web, visit<br>
> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
> or, via email, send a message with subject or body 'help' to<br>
> <a href="mailto:pw_forum-request@pwscf.org">pw_forum-request@pwscf.org</a><br>
><br>
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><br>
> When replying, please edit your Subject line so it is more specific<br>
> than "Re: Contents of Pw_forum digest..."<br>
><br>
><br>
> Today's Topics:<br>
><br>
> 1. Re: error loading shared libraries on parallel execution (Duy Le)<br>
> 2. pw.x running but nothing happens (wangqj1)<br>
> 3. Re: error loading shared libraries on parallel execution<br>
> (Bipul Rakshit)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Sat, 5 Sep 2009 19:39:17 -0400<br>
> From: Duy Le <<a href="mailto:ttduyle@gmail.com">ttduyle@gmail.com</a>><br>
> Subject: Re: [Pw_forum] error loading shared libraries on parallel<br>
> execution<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <<a href="mailto:8974d3b20909051639u575aed19xdf474c53f9a7d877@mail.gmail.com">8974d3b20909051639u575aed19xdf474c53f9a7d877@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Hi,I am not sure if this help. Could you please try to add<br>
> #$ -V in your submitting script. Like this:<br>
><br>
> #!/bin/bash<br>
> #<br>
> #$ -V<br>
> #$ -cwd<br>
> #$ -j y<br>
> #$ -S /bin/bash<br>
> #<br>
><br>
> Good luck.<br>
> D.<br>
><br>
> On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti<br>
> <<a href="mailto:colonel.sreekar@gmail.com">colonel.sreekar@gmail.com</a>>wrote:<br>
><br>
> > i know this issuehas been addressed and documented in troubleshooting<br>
> > section of the users guide.<br>
> > but i giveup in despair trying for a whole day to figure this problem<br>
> > i run my jobs on rocks cluster by using SGE's facility of submitting<br>
> batch<br>
> > jobs<br>
> ><br>
> ><br>
> <a href="http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html" target="_blank">http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html</a><br>
> ><br>
> > what i 'apparently' observe(or doubtfully infer) is that i can<br>
> successfully<br>
> > run a single parallel job, but on submitting a second job i get the error<br>
> > ____________________________________________<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > ____________________________________________<br>
> ><br>
> ><br>
> > i find out the path for the library and added to the LD_LIBRARY_PATH by<br>
> > writing<br>
> > _______________________________________<br>
> > #set the library path to include gfortran libraries<br>
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib<br>
> ><br>
> ><br>
> > $ECHO<br>
> > $ECHO "$LD_LIBRARY_PATH"<br>
> > $ECHO<br>
> > _______________________________________<br>
> ><br>
> > in the file which acts as script for qsub ($qsub -pe orte 4<br>
> > dosroutine.qsub) which is<br>
> ><br>
> > dosroutine.qsub<br>
> > -----------------------------------------------------------------<br>
> ><br>
> > #!/bin/bash<br>
> > #<br>
> > #$ -cwd<br>
> > #$ -j y<br>
> > #$ -S /bin/bash<br>
> > #<br>
> ><br>
> > #extract the info about no of processors involved from command line<br>
> > arguments of 'qsub'<br>
> > PROCESSORS=$NSLOTS<br>
> ><br>
> > #heuristically assign the no of processors per pool NPR<br>
> > NPR=4<br>
> > #as a result no of pools are give by<br>
> > NPK=`expr $PROCESSORS / $NPR`<br>
> ><br>
> > #!/bin/bash<br>
> > #<br>
> > #<br>
> > #Script for performing a dos calculation on a parallel processor<br>
> > WORKINGDIR=`pwd`<br>
> > ECHO="echo"<br>
> ><br>
> > #set the library path to include gfortran libraries<br>
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib<br>
> ><br>
> ><br>
> > $ECHO<br>
> > $ECHO "$LD_LIBRARY_PATH"<br>
> > $ECHO<br>
> ><br>
> > # set the needed environment variables<br>
> ><br>
> > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd`<br>
> > $ECHO $PREFIX<br>
> > BIN_DIR=$PREFIX/bin<br>
> > PSEUDO_DIR=$PREFIX/pseudo<br>
> > TMP_DIR=$HOME/tmp<br>
> > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS"<br>
> > PARA_POSTFIX="-npool $NPK"<br>
> ><br>
> > # required executables and pseudopotentials<br>
> > $ECHO<br>
> > $ECHO " executables directory: $BIN_DIR"<br>
> > $ECHO " pseudo directory: $PSEUDO_DIR"<br>
> > $ECHO " temporary directory: $TMP_DIR"<br>
> ><br>
> > #create results directory<br>
> > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do<br>
> > if test ! -d $DIR ; then<br>
> > mkdir $DIR<br>
> > fi<br>
> > done<br>
> > cd $WORKINGDIR/results<br>
> ><br>
> ><br>
> > # variables to represent programs<br>
> > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"<br>
> > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"<br>
> > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"<br>
> ><br>
> ><br>
> > # DOS calculation for 0Ni0<br>
> > cat > <a href="http://0ni0.dos.in" target="_blank">0ni0.dos.in</a> << EOF<br>
> > &control<br>
> > calculation='nscf'<br>
> > restart_mode='from_scratch',<br>
> > prefix='0ni0',<br>
> > pseudo_dir = '$PSEUDO_DIR/',<br>
> > outdir='$TMP_DIR/'<br>
> > /<br>
> > &system<br>
> > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,<br>
> > nspin = 2, starting_magnetization(1)=0.7,<br>
> > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8,<br>
> > occupations='tetrahedra'<br>
> > /<br>
> > &electrons<br>
> > conv_thr = 1.0e-10<br>
> > mixing_beta = 0.7<br>
> > /<br>
> > ATOMIC_SPECIES<br>
> > Ni 58.69 NiUS.RRKJ3.UPF<br>
> > ATOMIC_POSITIONS<br>
> > Ni 0.0 0.0 0.0<br>
> > K_POINTS {automatic} !special points generated by tetrahedra<br>
> method<br>
> > 12 12 12 0 0 0<br>
> > EOF<br>
> ><br>
> > $ECHO " running DOS calculation for 0Ni0 ...\c"<br>
> > $PW_COMMAND < <a href="http://0ni0.dos.in" target="_blank">0ni0.dos.in</a> > 0ni0.dos.out<br>
> > $ECHO<br>
> > $ECHO " done"<br>
> ><br>
> > -------------------------------------------------------------<br>
> ><br>
> > the output i get is<br>
> ><br>
> > ************************************************<br>
> > :/usr/lib64:/usr/lib<br>
> ><br>
> > /home3/colonel/espresso-4.0.5<br>
> ><br>
> > executables directory: /home3/colonel/espresso-4.0.5/bin<br>
> > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo<br>
> > temporary directory: /home3/colonel/tmp<br>
> > running DOS calculation for 0Ni0 ...\c<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> ><br>
> > done<br>
> > *************************************************<br>
> > plz suggest solutions which donot require root permissions , as i dont<br>
> have<br>
> > thanks in advance<br>
> > --<br>
> > Sreekar Guddeti<br>
> > Department of Physics<br>
> ><br>
> > _______________________________________________<br>
> > Pw_forum mailing list<br>
> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
> ><br>
> ><br>
><br>
><br>
> --<br>
> --------------------------------------------------<br>
> Duy Le<br>
> PhD Student<br>
> Department of Physics<br>
> University of Central Florida.<br>
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><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST)<br>
> From: wangqj1 <<a href="mailto:wangqj1@126.com">wangqj1@126.com</a>><br>
> Subject: [Pw_forum] pw.x running but nothing happens<br>
> To: pw_forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <<a href="mailto:25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com">25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com</a>><br>
> Content-Type: text/plain; charset="gbk"<br>
><br>
><br>
> Dear pwscf users<br>
> When I run vc-relax on the computing cluster use one node which has 8<br>
> CPUs.<br>
> The output file is as following:<br>
><br>
> Program PWSCF v.4.0.1 starts ...<br>
> Today is 6Sep2009 at 7:49:30<br>
> Parallel version (MPI)<br>
> Number of processors in use: 8<br>
> R & G space division: proc/pool = 8<br>
> For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW<br>
> .....................................................................<br>
> Initial potential from superposition of free atoms<br>
> starting charge 435.99565, renormalised to 436.00000<br>
> Starting wfc are 254 atomic + 8 random wfc<br>
><br>
> After one day ,it still like this and no iteration has completed ,there is<br>
> also no error was turn up .There is no error in the input file because I<br>
> have test it on anthoer computer which has 4 CPUs and it runs well .<br>
> I can't find the reason about this ,any help will be appreciated .<br>
> Best Regards<br>
> Q.J.Wang<br>
> XiangTan University<br>
><br>
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><br>
> ------------------------------<br>
><br>
> Message: 3<br>
> Date: Sun, 6 Sep 2009 07:58:49 +0100<br>
> From: Bipul Rakshit <<a href="mailto:bipulrr@gmail.com">bipulrr@gmail.com</a>><br>
> Subject: Re: [Pw_forum] error loading shared libraries on parallel<br>
> execution<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID: <<a href="mailto:3a749910909052358m6f23c3sf5bdbba1b595d8d5@mail.gmail.com">3a749910909052358m6f23c3sf5bdbba1b595d8d5@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> hi,<br>
> Just from root user type<br>
> yum install libgfortran.so.3<br>
><br>
> then it will install this files which is not present in your machine<br>
><br>
> On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti<br>
> <<a href="mailto:colonel.sreekar@gmail.com">colonel.sreekar@gmail.com</a>>wrote:<br>
><br>
> > i know this issuehas been addressed and documented in troubleshooting<br>
> > section of the users guide.<br>
> > but i giveup in despair trying for a whole day to figure this problem<br>
> > i run my jobs on rocks cluster by using SGE's facility of submitting<br>
> batch<br>
> > jobs<br>
> ><br>
> ><br>
> <a href="http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html" target="_blank">http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html</a><br>
> ><br>
> > what i 'apparently' observe(or doubtfully infer) is that i can<br>
> successfully<br>
> > run a single parallel job, but on submitting a second job i get the error<br>
> > ____________________________________________<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > ____________________________________________<br>
> ><br>
> ><br>
> > i find out the path for the library and added to the LD_LIBRARY_PATH by<br>
> > writing<br>
> > _______________________________________<br>
> > #set the library path to include gfortran libraries<br>
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib<br>
> ><br>
> ><br>
> > $ECHO<br>
> > $ECHO "$LD_LIBRARY_PATH"<br>
> > $ECHO<br>
> > _______________________________________<br>
> ><br>
> > in the file which acts as script for qsub ($qsub -pe orte 4<br>
> > dosroutine.qsub) which is<br>
> ><br>
> > dosroutine.qsub<br>
> > -----------------------------------------------------------------<br>
> ><br>
> > #!/bin/bash<br>
> > #<br>
> > #$ -cwd<br>
> > #$ -j y<br>
> > #$ -S /bin/bash<br>
> > #<br>
> ><br>
> > #extract the info about no of processors involved from command line<br>
> > arguments of 'qsub'<br>
> > PROCESSORS=$NSLOTS<br>
> ><br>
> > #heuristically assign the no of processors per pool NPR<br>
> > NPR=4<br>
> > #as a result no of pools are give by<br>
> > NPK=`expr $PROCESSORS / $NPR`<br>
> ><br>
> > #!/bin/bash<br>
> > #<br>
> > #<br>
> > #Script for performing a dos calculation on a parallel processor<br>
> > WORKINGDIR=`pwd`<br>
> > ECHO="echo"<br>
> ><br>
> > #set the library path to include gfortran libraries<br>
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib<br>
> ><br>
> ><br>
> > $ECHO<br>
> > $ECHO "$LD_LIBRARY_PATH"<br>
> > $ECHO<br>
> ><br>
> > # set the needed environment variables<br>
> ><br>
> > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd`<br>
> > $ECHO $PREFIX<br>
> > BIN_DIR=$PREFIX/bin<br>
> > PSEUDO_DIR=$PREFIX/pseudo<br>
> > TMP_DIR=$HOME/tmp<br>
> > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS"<br>
> > PARA_POSTFIX="-npool $NPK"<br>
> ><br>
> > # required executables and pseudopotentials<br>
> > $ECHO<br>
> > $ECHO " executables directory: $BIN_DIR"<br>
> > $ECHO " pseudo directory: $PSEUDO_DIR"<br>
> > $ECHO " temporary directory: $TMP_DIR"<br>
> ><br>
> > #create results directory<br>
> > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do<br>
> > if test ! -d $DIR ; then<br>
> > mkdir $DIR<br>
> > fi<br>
> > done<br>
> > cd $WORKINGDIR/results<br>
> ><br>
> ><br>
> > # variables to represent programs<br>
> > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"<br>
> > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"<br>
> > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"<br>
> ><br>
> ><br>
> > # DOS calculation for 0Ni0<br>
> > cat > <a href="http://0ni0.dos.in" target="_blank">0ni0.dos.in</a> << EOF<br>
> > &control<br>
> > calculation='nscf'<br>
> > restart_mode='from_scratch',<br>
> > prefix='0ni0',<br>
> > pseudo_dir = '$PSEUDO_DIR/',<br>
> > outdir='$TMP_DIR/'<br>
> > /<br>
> > &system<br>
> > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,<br>
> > nspin = 2, starting_magnetization(1)=0.7,<br>
> > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8,<br>
> > occupations='tetrahedra'<br>
> > /<br>
> > &electrons<br>
> > conv_thr = 1.0e-10<br>
> > mixing_beta = 0.7<br>
> > /<br>
> > ATOMIC_SPECIES<br>
> > Ni 58.69 NiUS.RRKJ3.UPF<br>
> > ATOMIC_POSITIONS<br>
> > Ni 0.0 0.0 0.0<br>
> > K_POINTS {automatic} !special points generated by tetrahedra<br>
> method<br>
> > 12 12 12 0 0 0<br>
> > EOF<br>
> ><br>
> > $ECHO " running DOS calculation for 0Ni0 ...\c"<br>
> > $PW_COMMAND < <a href="http://0ni0.dos.in" target="_blank">0ni0.dos.in</a> > 0ni0.dos.out<br>
> > $ECHO<br>
> > $ECHO " done"<br>
> ><br>
> > -------------------------------------------------------------<br>
> ><br>
> > the output i get is<br>
> ><br>
> > ************************************************<br>
> > :/usr/lib64:/usr/lib<br>
> ><br>
> > /home3/colonel/espresso-4.0.5<br>
> ><br>
> > executables directory: /home3/colonel/espresso-4.0.5/bin<br>
> > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo<br>
> > temporary directory: /home3/colonel/tmp<br>
> > running DOS calculation for 0Ni0 ...\c<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared<br>
> > libraries: libgfortran.so.3: cannot open shared object file: No such<br>
> > file or directory<br>
> ><br>
> > done<br>
> > *************************************************<br>
> > plz suggest solutions which donot require root permissions , as i dont<br>
> have<br>
> > thanks in advance<br>
> > --<br>
> > Sreekar Guddeti<br>
> > Department of Physics<br>
> ><br>
> > _______________________________________________<br>
> > Pw_forum mailing list<br>
> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
> ><br>
> ><br>
><br>
><br>
> --<br>
> Dr. Bipul Rakshit<br>
> Research Associate,<br>
> S N Bose Centre for Basic Sciences,<br>
> Salt Lake,<br>
> Kolkata 700 098<br>
> India<br>
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><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
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><br>
><br>
> End of Pw_forum Digest, Vol 27, Issue 23<br>
> ****************************************<br>
><br>
<br>
<br>
<br>
--<br>
Sreekar Guddeti<br>
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End of Pw_forum Digest, Vol 27, Issue 24<br>
****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Sreekar Guddeti<br><br>