[Pw_forum] Pw_forum Digest, Vol 27, Issue 26
Stefano Baroni
baroni at sissa.it
Mon Sep 7 08:42:40 CEST 2009
please, in order to make the life of those who may want to help you
easier:
1) always indicate the subject of your post in the "subject" field.
the more accurate the short description of your problem, the easier it
will be that somebody will pick your post up
2) group all the questions related to a same problem in a same post.
the time that each of us devotes voluntarily to this community
activity is limited. the easier it is to go through the forum, the
highest are the chances that some relevant questions are answered.
3) strip unrelated material from the post. I understand that composing
a regular mail massege may take 2-3 seconds more than just hitting
"reply", but I think that this time is worth avoiding cluttering our
mail boxes with garbage.
this being said, I am not the most appropriate person to pick up your
answers. I wish somebody else will ...
best wishes - Stefano Baroni
On Sep 7, 2009, at 4:25 AM, sreekar guddeti wrote:
> sorry for making repeated posts but on
> $./configure --enable-parallel --host=x86_64
> configuration is successful for parallel version
> on $make all
> in the compilation report i get the following warnings related to
> libgfortran.so.3 and no other warnings
>
> /usr/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/
> libmpi_f90.so, may conflict with libgfortran.so.3 ( 8 times)
>
> /usr/bin/ld: warning: libgfortran.so.1, needed by /usr/lib/gcc/
> x86_64-redhat-linux6E/4.3.2/../../../liblapack.a, may conflict with
> libgfortran.so.3 (many times)
>
> hope this information is useful for suggesting a solution to the
> problem
> sincerely,
> sreekar guddeti
> Dept.Physics
> IIT Bombay
> India
>
> On Mon, Sep 7, 2009 at 6:36 AM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
> pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
> pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
> pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
> 1. Re: Pw_forum Digest, Vol 27, Issue 25 (sreekar guddeti)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 7 Sep 2009 06:36:10 +0530
> From: sreekar guddeti <colonel.sreekar at gmail.com>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 25
> To: pw_forum at pwscf.org
> Message-ID:
> <c864e4460909061806j5cde75efk76af1e8dba08d111 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> > As an alternative, try static
> > link (add -static to LDFLAGS in make.sys).
>
> The other thing that i tried was
> $make clean
> $./configure --enable-parallel --disable-shared --host=x86_64
>
> output is
> ___________________________________________
> configure: WARNING: If you wanted to set the --build type, don't use
> --host.
> If a cross compiler is detected then cross compile mode will be
> used.
> checking build system type... x86_64-unknown-linux-gnu
> configure: WARNING: incorrect host name ?
> checking architecture...
> configure: WARNING: unsupported architecture?
> checking for x86_64-g95... no
> checking for x86_64-gfortran... no
> checking for x86_64-f90... no
> checking for g95... no
> checking for gfortran... gfortran
> checking for Fortran 77 compiler default output file name... a.out
> checking whether the Fortran 77 compiler works... yes
> checking whether we are cross compiling... yes
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran accepts -g... yes
> checking for x86_64-mpif90... no
> checking for x86_64-gfortran... no
> checking for mpif90... mpif90
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether mpif90 accepts -g... yes
> setting F90... gfortran
> setting MPIF90... mpif90
> checking for x86_64-cc... no
> checking for x86_64-gcc... no
> checking for cc... no
> checking for gcc... gcc
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> setting CC... gcc
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for int *... yes
> checking size of int *... 8
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for struct mallinfo.arena... yes
> checking for x86_64-gfortran... no
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran accepts -g... yes
> setting F77... gfortran
> using F90... gfortran
> setting FFLAGS... -O3
> setting F90FLAGS... $(FFLAGS) -x f95-cpp-input
> setting FFLAGS_NOOPT... -O0
> setting CFLAGS... -O3
> setting CPP... cpp
> setting CPPFLAGS... -P -traditional
> setting LD... mpif90
> setting LDFLAGS... -static
> setting AR... ar
> setting ARFLAGS... ruv
> setting ARFLAGS_DYNAMIC...ruv
> checking whether make sets $(MAKE)... yes
> checking whether Fortran files must be preprocessed... no
> checking how to get verbose linking output from gfortran... -v
> checking for Fortran libraries of gfortran...
> -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2
> -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64 -L/
> lib/../lib64
> -L/usr/lib/../lib64 -L/opt/intel/Compiler/11.1/046/lib/intel64
> -L/opt/intel/Compiler/11.1/046/ipp/em64t/lib
> -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t
> -L/opt/intel/Compiler/11.1/046/tbb/em64t/
> cc4.1.0_libc2.4_kernel2.6.16.21/lib
> -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../.. -lgfortranbegin
> -lgfortran -lm -lgcc_s
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore,
> no
> extra underscore
> checking for library containing dgemm... no
> in /usr/local/lib: checking for library containing dgemm... no
> in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library
> containing
> dgemm... no
> in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for
> library
> containing dgemm... no
> in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library
> containing dgemm... no
> in
> /opt/intel/Compiler/11.1/046/tbb/em64t/
> cc4.1.0_libc2.4_kernel2.6.16.21/lib:
> checking for library containing dgemm... no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> dgemm...
> no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> dgemm...
> no
> checking for library containing dgemm... no
> in /usr/local/lib: checking for library containing dgemm... no
> in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library
> containing
> dgemm... no
> in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for
> library
> containing dgemm... no
> in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library
> containing dgemm... no
> in
> /opt/intel/Compiler/11.1/046/tbb/em64t/
> cc4.1.0_libc2.4_kernel2.6.16.21/lib:
> checking for library containing dgemm... no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> dgemm...
> no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> dgemm...
> no
> checking for library containing zggev... no
> in /usr/local/lib: checking for library containing zggev... no
> in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library
> containing
> zggev... no
> in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for
> library
> containing zggev... no
> in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library
> containing zggev... no
> in
> /opt/intel/Compiler/11.1/046/tbb/em64t/
> cc4.1.0_libc2.4_kernel2.6.16.21/lib:
> checking for library containing zggev... no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> zggev...
> no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> zggev...
> no
> setting BLAS_LIBS... ../flib/blas.a
> setting LAPACK_LIBS... ../flib/lapack.a
> checking for library containing fftwnd... no
> in /usr/local/lib: checking for library containing fftwnd... no
> in /cineca/prod/gnu/lib: checking for library containing fftwnd... no
> in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library
> containing
> fftwnd... no
> in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for
> library
> containing fftwnd... no
> in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library
> containing fftwnd... no
> in
> /opt/intel/Compiler/11.1/046/tbb/em64t/
> cc4.1.0_libc2.4_kernel2.6.16.21/lib:
> checking for library containing fftwnd... no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> fftwnd...
> no
> in /opt/gridengine/lib/lx26-amd64: checking for library containing
> fftwnd...
> no
> setting FFT_LIBS...
> checking for library containing fftwnd... (cached) no
> setting MASS_LIBS...
> checking for library containing mpi_init... no
> setting MPI_LIBS...
> checking for library containing mpi_init... (cached) no
> setting DFLAGS... -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW
> setting IFLAGS... -I../include
> setting FDFLAGS... $(DFLAGS)
> setting RANLIB... echo
> configure: creating ./config.status
> config.status: creating include/fft_defs.h
> config.status: creating make.sys
> config.status: creating configure.msg
> config.status: creating include/c_defs.h
> config.status: include/c_defs.h is unchanged
> --------------------------------------------------------------------
> ESPRESSO can take advantage of several optimized numerical libraries
> (essl, fftw, mkl...). This configure script attempts to find them,
> but may fail if they have been installed in non-standard locations.
> If a required library is not found, the local copy will be compiled.
>
> The following libraries have been found:
> BLAS_LIBS=../flib/blas.a
> LAPACK_LIBS=../flib/lapack.a
> FFT_LIBS=
> Please check if this is what you expect.
>
> If any libraries are missing, you may specify a list of directories
> to search and retry, as follows:
> ./configure LIBDIRS="list of directories, separated by spaces"
>
> Parallel environment not detected (is this a parallel machine?).
> Configured for compilation of serial executables.
>
> For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).
> --------------------------------------------------------------------
> configure: success
> ______________________________________________
>
> but parallel version is not getting compiled
>
>
> sincerely,
> Sreekar Guddeti
> Dept. Physics
> IIT Bombay
> India
>
>
>
>
> On Mon, Sep 7, 2009 at 5:23 AM, <pw_forum-request at pwscf.org> wrote:
>
> > Send Pw_forum mailing list submissions to
> > pw_forum at pwscf.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://www.democritos.it/mailman/listinfo/pw_forum
> > or, via email, send a message with subject or body 'help' to
> > pw_forum-request at pwscf.org
> >
> > You can reach the person managing the list at
> > pw_forum-owner at pwscf.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pw_forum digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: Pw_forum Digest, Vol 27, Issue 24 (sreekar guddeti)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Sep 2009 05:23:12 +0530
> > From: sreekar guddeti <colonel.sreekar at gmail.com>
> > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 24
> > To: pw_forum at pwscf.org
> > Message-ID:
> > <c864e4460909061653j5cfaea62t9e77de6d42dba9da at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > i have set variable LD_FLAGS = static in make.sys file
> >
> > and on $make all
> >
> > i get error
> > ----------------------------------------
> > libiotk.a
> > 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
> > make loclib_only
> > make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src'
> > make[3]: Nothing to be done for `loclib_only'.
> > make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src'
> > mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a
> > /opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open':
> > (.text+0x123): warning: Using 'dlopen' in statically linked
> applications
> > requires at runtime the shared libraries from the glibc version
> used for
> > linking
> > /opt/openmpi/lib/libopen-rte.a(sys_info.o): In function
> `orte_sys_info':
> > (.text+0x16f): warning: Using 'getpwuid' in statically linked
> applications
> > requires at runtime the shared libraries from the glibc version
> used for
> > linking
> > /opt/openmpi/lib/libopen-pal.a(if.o): In function
> `opal_ifaddrtoname':
> > (.text+0x780): warning: Using 'gethostbyname' in statically linked
> > applications requires at runtime the shared libraries from the glibc
> > version
> > used for linking
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `__malloc_check_init':
> > (.text+0x1060): multiple definition of `__malloc_check_init'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `_int_free':
> > (.text+0x2230): multiple definition of `_int_free'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `_int_malloc':
> > (.text+0x2a50): multiple definition of `_int_malloc'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `_int_memalign':
> > (.text+0x3900): multiple definition of `_int_memalign'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `_int_valloc':
> > (.text+0x3c30): multiple definition of `_int_valloc'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `_int_realloc':
> > (.text+0x3d80): multiple definition of `_int_realloc'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `free':
> > (.text+0x5f20): multiple definition of `free'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `malloc':
> > (.text+0x4690): multiple definition of `malloc'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first
> defined
> > here
> > /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)
> >
> > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/
> libc.a(malloc.o):
> > In function `realloc':
> > (.text+0x60f0): multiple definition of `realloc'
> > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first
> defined
> > here
> > /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)
> > collect2: ld returned 1 exit status
> > make[2]: *** [iotk_print_kinds.x] Error 1
> > make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src'
> > make[1]: *** [lib+util] Error 2
> > make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk'
> > make: *** [libiotk] Error 2
> >
> > ---------------------------------------------
> >
> > sincerely
> >
> >
> > On Sun, Sep 6, 2009 at 11:35 PM, <pw_forum-request at pwscf.org> wrote:
> >
> > > Send Pw_forum mailing list submissions to
> > > pw_forum at pwscf.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > or, via email, send a message with subject or body 'help' to
> > > pw_forum-request at pwscf.org
> > >
> > > You can reach the person managing the list at
> > > pw_forum-owner at pwscf.org
> > >
> > > When replying, please edit your Subject line so it is more
> specific
> > > than "Re: Contents of Pw_forum digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: pw.x running but nothing happens (Bipul Rakshit)
> > > 2. pseudo potential (Mansoureh Pashangpour)
> > > 3. Re: error loading shared libraries on parallel execution
> > > (Paolo Giannozzi)
> > > 4. Re: pw.x running but nothing happens (Lorenzo Paulatto)
> > > 5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti)
> > >
> > >
> > >
> ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Sun, 6 Sep 2009 08:03:29 +0100
> > > From: Bipul Rakshit <bipulrr at gmail.com>
> > > Subject: Re: [Pw_forum] pw.x running but nothing happens
> > > To: PWSCF Forum <pw_forum at pwscf.org>
> > > Message-ID:
> > >
> <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com>
> > > Content-Type: text/plain; charset="gb2312"
> > >
> > > Dear Wangqj,
> > > The same thing happens to me.
> > > since you are using large no. of wfc, although it shows the job is
> > running
> > > in 8 procs, but sometimes if the installation is not proper, it is
> > running
> > > in 1 procs only.
> > >
> > > So better you check the parallel installation using a small job,
> with
> > > different no. of procs and see whether its taking lesser time
> as no. of
> > > procs increases or not?
> > >
> > > cheers
> > >
> > > 2009/9/6 wangqj1 <wangqj1 at 126.com>
> > >
> > > >
> > > > Dear pwscf users
> > > > When I run vc-relax on the computing cluster use one node
> which
> > has
> > > 8
> > > > CPUs.
> > > > The output file is as following:
> > > >
> > > > Program PWSCF v.4.0.1 starts ...
> > > > Today is 6Sep2009 at 7:49:30
> > > > Parallel version (MPI)
> > > > Number of processors in use: 8
> > > > R & G space division: proc/pool = 8
> > > > For Norm-Conserving or Ultrasoft (Vanderbilt)
> Pseudopotentials or
> > > PAW
> > >
> >
> .....................................................................
> > > > Initial potential from superposition of free atoms
> > > > starting charge 435.99565, renormalised to 436.00000
> > > > Starting wfc are 254 atomic + 8 random wfc
> > > >
> > > > After one day ,it still like this and no iteration has
> completed ,there
> > > is
> > > > also no error was turn up .There is no error in the input file
> because
> > I
> > > > have test it on anthoer computer which has 4 CPUs and it runs
> well .
> > > > I can't find the reason about this ,any help will be
> appreciated .
> > > > Best Regards
> > > > Q.J.Wang
> > > > XiangTan University
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > > ???????????,www.yeah.net <http://www.yeah.net/?from=footer>
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > >
> > > >
> > >
> > >
> > > --
> > > Dr. Bipul Rakshit
> > > Research Associate,
> > > S N Bose Centre for Basic Sciences,
> > > Salt Lake,
> > > Kolkata 700 098
> > > India
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL:
> > >
> > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Sun, 6 Sep 2009 11:25:06 +0330
> > > From: Mansoureh Pashangpour <mansourehp at gmail.com>
> > > Subject: [Pw_forum] pseudo potential
> > > To: PWSCF Forum <pw_forum at pwscf.org>
> > > Message-ID:
> > > <cbe1626b0909060055o66690789yc0ae02efdfa5391e at mail.gmail.com
> >
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Dear all
> > > how can I plot these pseudo potentials? how can I discribe the
> > properties
> > > of pseudo potentials?
> > >
> > > *Fe.pbe-nd-rrkjus.UPF*<
> > > http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF>
> > > (
> > > *details*<
> > > http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF
> >)
> > >
> > >
> > > Perdew-Burke-Ernzerhof (PBE) exch-corr
> > > nonlinear core-correction
> > > semicore state d in valence
> > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft)
> > >
> > > and
> > >
> > > *H.pbe-rrkjus.UPF* <http://www.pwscf.org/pseudo/1.3/UPF/H.pbe-rrkjus.UPF
> > >
> > > (*details* <
> > > http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>)
> > >
> > >
> > > Perdew-Burke-Ernzerhof (PBE) exch-corr
> > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft)
> > >
> > >
> > > and
> > >
> > > *O.pbe-rrkjus.UPF*
> > > <http://www.pwscf.org/pseudo/1.3/UPF/O.pbe-rrkjus.UPF>
> (*details*
> > > <http://www.pwscf.org/pseudo/upfdetails.php?upf=O.pbe-rrkjus.UPF>)
> > >
> > > Perdew-Burke-Ernzerhof (PBE) exch-corr
> > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft)
> > >
> > >
> > > Thanks
> > > Mansoureh Pashangpour
> > > Ph.D student
> > > Islami Azad university
> > > science & reaserch branch
> > > Tehran, IRAN
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL:
> > >
> > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Sun, 6 Sep 2009 10:24:48 +0200
> > > From: Paolo Giannozzi <giannozz at democritos.it>
> > > Subject: Re: [Pw_forum] error loading shared libraries on parallel
> > > execution
> > > To: PWSCF Forum <pw_forum at pwscf.org>
> > > Message-ID: <E6918F77-0C97-4F26-9F7E-BE790E9EFC6B at democritos.it>
> > > Content-Type: text/plain; charset=US-ASCII; format=flowed
> > >
> > >
> > > On Sep 6, 2009, at 1:20 , sreekar guddeti wrote:
> > >
> > > > plz suggest solutions which donot require root permissions ,
> > > > as i dont have
> > >
> > > somebody must have it. Report the problem and the
> > > solution (i.e. install gfortran on ALL processors) to
> > > whoever has root access. As an alternative, try static
> > > link (add -static to LDFLAGS in make.sys).
> > > ---
> > > Paolo Giannozzi, Dept of Physics, University of Udine
> > > via delle Scienze 208, 33100 Udine, Italy
> > > Phone +39-0432-558216, fax +39-0432-558222
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST)
> > > From: "Lorenzo Paulatto" <paulatto at sissa.it>
> > > Subject: Re: [Pw_forum] pw.x running but nothing happens
> > > To: "PWSCF Forum" <pw_forum at pwscf.org>
> > > Message-ID: <46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it
> >
> > > Content-Type: text/plain;charset=iso-8859-1
> > >
> > >
> > > On Sun, September 6, 2009 02:33, wangqj1 wrote:
> > > > After one day ,it still like this and no iteration has
> completed
> > ,there
> > > > is
> > > > also no error was turn up .There is no error in the input
> file because
> > I
> > > > have test it on anthoer computer which has 4 CPUs and it runs
> well .
> > > > I can't find the reason about this ,any help will be
> appreciated .
> > >
> > >
> > > Dear QJ,
> > > this is strange. But we would need more information on your
> hardwre
> > > configuration in order to help you. In the mean while you can
> check the
> > > behaviour of te pw.x processes with "top". E.g. if they are all
> runing at
> > > 100% CPU, how much memory they are taking and so on.
> > >
> > > regards
> > >
> > >
> > > --
> > > Lorenzo Paulatto
> > > SISSA & DEMOCRITOS (Trieste)
> > > phone: +39 040 3787 511
> > > skype: paulatz
> > > www: http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/
> >
> > <http://people.sissa.it/%7Epaulatto/>
> > >
> > >
> > >
> > > ----------------------------------------------------------------
> > > SISSA Webmail https://webmail.sissa.it/
> > > Powered by SquirrelMail http://www.squirrelmail.org/
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 5
> > > Date: Sun, 6 Sep 2009 23:35:26 +0530
> > > From: sreekar guddeti <colonel.sreekar at gmail.com>
> > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23
> > > To: pw_forum at pwscf.org
> > > Message-ID:
> > >
> <c864e4460909061105i43b1885dh6141b2789b8ae51 at mail.gmail.com>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > @duy lee
> > > i inserted the line #$ -V in my qsub script and the env variable
> > > $LD_LIBRARY_PATH is being set from script... thanks for that but
> still
> > > problem persists.
> > >
> > > @rakshit
> > >
> > > -----------------------------
> > > $find /usr/lib -name libgfortran*
> > > -----------------------------
> > > and output is
> > > _______________________
> > > /usr/lib/libgfortran.so.1.0.0
> > > /usr/lib/libgfortran.so.1
> > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a
> > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a
> > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so
> > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a
> > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a
> > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so
> > > _______________________
> > > whereas on doing
> > > -----------------------------
> > > $find /usr/lib64 -name libgfortran*
> > > -----------------------------
> > > ouput is
> > > _________________
> > > /usr/lib64/libgfortran.so.3.0.0
> > > /usr/lib64/libgfortran.so.1.0.0
> > > /usr/lib64/libgfortran.so.1
> > > find: /usr/lib64/audit: Permission denied
> > > */usr/lib64/libgfortran.so.3*
> > > _________________
> > >
> > > it means my OS has the required library, i guess
> > >
> > > i installed the QE on the head node
> > > This cluster is a Rocks cluster with
> > >
> > > # of nodes: 10 (1 head node + 9 compute nodes)
> > > # of processors/node: 8
> > > # Total # of processors: 10X8 = 80
> > >
> > > i tested the sample program for submitting batch jobs using SGE
> utility
> > and
> > > it is working fine(
> > >
> > >
> > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html
> > > )
> > >
> > > sincerely,
> > > sreekar guddeti
> > > Dept. Physics
> > > IIT Bombay
> > > India
> > >
> > >
> > > On Sun, Sep 6, 2009 at 12:28 PM, <pw_forum-request at pwscf.org>
> wrote:
> > >
> > > > Send Pw_forum mailing list submissions to
> > > > pw_forum at pwscf.org
> > > >
> > > > To subscribe or unsubscribe via the World Wide Web, visit
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > > or, via email, send a message with subject or body 'help' to
> > > > pw_forum-request at pwscf.org
> > > >
> > > > You can reach the person managing the list at
> > > > pw_forum-owner at pwscf.org
> > > >
> > > > When replying, please edit your Subject line so it is more
> specific
> > > > than "Re: Contents of Pw_forum digest..."
> > > >
> > > >
> > > > Today's Topics:
> > > >
> > > > 1. Re: error loading shared libraries on parallel execution
> (Duy Le)
> > > > 2. pw.x running but nothing happens (wangqj1)
> > > > 3. Re: error loading shared libraries on parallel execution
> > > > (Bipul Rakshit)
> > > >
> > > >
> > > >
> ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Sat, 5 Sep 2009 19:39:17 -0400
> > > > From: Duy Le <ttduyle at gmail.com>
> > > > Subject: Re: [Pw_forum] error loading shared libraries on
> parallel
> > > > execution
> > > > To: PWSCF Forum <pw_forum at pwscf.org>
> > > > Message-ID:
> > > > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com
> >
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Hi,I am not sure if this help. Could you please try to add
> > > > #$ -V in your submitting script. Like this:
> > > >
> > > > #!/bin/bash
> > > > #
> > > > #$ -V
> > > > #$ -cwd
> > > > #$ -j y
> > > > #$ -S /bin/bash
> > > > #
> > > >
> > > > Good luck.
> > > > D.
> > > >
> > > > On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti
> > > > <colonel.sreekar at gmail.com>wrote:
> > > >
> > > > > i know this issuehas been addressed and documented in
> troubleshooting
> > > > > section of the users guide.
> > > > > but i giveup in despair trying for a whole day to figure
> this problem
> > > > > i run my jobs on rocks cluster by using SGE's facility of
> submitting
> > > > batch
> > > > > jobs
> > > > >
> > > > >
> > > >
> > >
> > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html
> > > > >
> > > > > what i 'apparently' observe(or doubtfully infer) is that i can
> > > > successfully
> > > > > run a single parallel job, but on submitting a second job i
> get the
> > > error
> > > > > ____________________________________________
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > ____________________________________________
> > > > >
> > > > >
> > > > > i find out the path for the library and added to the
> LD_LIBRARY_PATH
> > by
> > > > > writing
> > > > > _______________________________________
> > > > > #set the library path to include gfortran libraries
> > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
> > > > >
> > > > >
> > > > > $ECHO
> > > > > $ECHO "$LD_LIBRARY_PATH"
> > > > > $ECHO
> > > > > _______________________________________
> > > > >
> > > > > in the file which acts as script for qsub ($qsub -pe orte 4
> > > > > dosroutine.qsub) which is
> > > > >
> > > > > dosroutine.qsub
> > > > >
> -----------------------------------------------------------------
> > > > >
> > > > > #!/bin/bash
> > > > > #
> > > > > #$ -cwd
> > > > > #$ -j y
> > > > > #$ -S /bin/bash
> > > > > #
> > > > >
> > > > > #extract the info about no of processors involved from
> command line
> > > > > arguments of 'qsub'
> > > > > PROCESSORS=$NSLOTS
> > > > >
> > > > > #heuristically assign the no of processors per pool NPR
> > > > > NPR=4
> > > > > #as a result no of pools are give by
> > > > > NPK=`expr $PROCESSORS / $NPR`
> > > > >
> > > > > #!/bin/bash
> > > > > #
> > > > > #
> > > > > #Script for performing a dos calculation on a parallel
> processor
> > > > > WORKINGDIR=`pwd`
> > > > > ECHO="echo"
> > > > >
> > > > > #set the library path to include gfortran libraries
> > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
> > > > >
> > > > >
> > > > > $ECHO
> > > > > $ECHO "$LD_LIBRARY_PATH"
> > > > > $ECHO
> > > > >
> > > > > # set the needed environment variables
> > > > >
> > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd`
> > > > > $ECHO $PREFIX
> > > > > BIN_DIR=$PREFIX/bin
> > > > > PSEUDO_DIR=$PREFIX/pseudo
> > > > > TMP_DIR=$HOME/tmp
> > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS"
> > > > > PARA_POSTFIX="-npool $NPK"
> > > > >
> > > > > # required executables and pseudopotentials
> > > > > $ECHO
> > > > > $ECHO " executables directory: $BIN_DIR"
> > > > > $ECHO " pseudo directory: $PSEUDO_DIR"
> > > > > $ECHO " temporary directory: $TMP_DIR"
> > > > >
> > > > > #create results directory
> > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do
> > > > > if test ! -d $DIR ; then
> > > > > mkdir $DIR
> > > > > fi
> > > > > done
> > > > > cd $WORKINGDIR/results
> > > > >
> > > > >
> > > > > # variables to represent programs
> > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
> > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
> > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x
> $PARA_POSTFIX"
> > > > >
> > > > >
> > > > > # DOS calculation for 0Ni0
> > > > > cat > 0ni0.dos.in << EOF
> > > > > &control
> > > > > calculation='nscf'
> > > > > restart_mode='from_scratch',
> > > > > prefix='0ni0',
> > > > > pseudo_dir = '$PSEUDO_DIR/',
> > > > > outdir='$TMP_DIR/'
> > > > > /
> > > > > &system
> > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,
> > > > > nspin = 2, starting_magnetization(1)=0.7,
> > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8,
> > > > > occupations='tetrahedra'
> > > > > /
> > > > > &electrons
> > > > > conv_thr = 1.0e-10
> > > > > mixing_beta = 0.7
> > > > > /
> > > > > ATOMIC_SPECIES
> > > > > Ni 58.69 NiUS.RRKJ3.UPF
> > > > > ATOMIC_POSITIONS
> > > > > Ni 0.0 0.0 0.0
> > > > > K_POINTS {automatic} !special points generated by
> tetrahedra
> > > > method
> > > > > 12 12 12 0 0 0
> > > > > EOF
> > > > >
> > > > > $ECHO " running DOS calculation for 0Ni0 ...\c"
> > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out
> > > > > $ECHO
> > > > > $ECHO " done"
> > > > >
> > > > > -------------------------------------------------------------
> > > > >
> > > > > the output i get is
> > > > >
> > > > > ************************************************
> > > > > :/usr/lib64:/usr/lib
> > > > >
> > > > > /home3/colonel/espresso-4.0.5
> > > > >
> > > > > executables directory: /home3/colonel/espresso-4.0.5/bin
> > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo
> > > > > temporary directory: /home3/colonel/tmp
> > > > > running DOS calculation for 0Ni0 ...\c
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > >
> > > > > done
> > > > > *************************************************
> > > > > plz suggest solutions which donot require root permissions ,
> as i
> > dont
> > > > have
> > > > > thanks in advance
> > > > > --
> > > > > Sreekar Guddeti
> > > > > Department of Physics
> > > > >
> > > > > _______________________________________________
> > > > > Pw_forum mailing list
> > > > > Pw_forum at pwscf.org
> > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > --------------------------------------------------
> > > > Duy Le
> > > > PhD Student
> > > > Department of Physics
> > > > University of Central Florida.
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL:
> > > >
> > >
> > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 2
> > > > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST)
> > > > From: wangqj1 <wangqj1 at 126.com>
> > > > Subject: [Pw_forum] pw.x running but nothing happens
> > > > To: pw_forum <pw_forum at pwscf.org>
> > > > Message-ID:
> > > > <
> > 25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com
> > > >
> > > > Content-Type: text/plain; charset="gbk"
> > > >
> > > >
> > > > Dear pwscf users
> > > > When I run vc-relax on the computing cluster use one node
> which has
> > 8
> > > > CPUs.
> > > > The output file is as following:
> > > >
> > > > Program PWSCF v.4.0.1 starts ...
> > > > Today is 6Sep2009 at 7:49:30
> > > > Parallel version (MPI)
> > > > Number of processors in use: 8
> > > > R & G space division: proc/pool = 8
> > > > For Norm-Conserving or Ultrasoft (Vanderbilt)
> Pseudopotentials or
> > PAW
> > >
> >
> .....................................................................
> > > > Initial potential from superposition of free atoms
> > > > starting charge 435.99565, renormalised to 436.00000
> > > > Starting wfc are 254 atomic + 8 random wfc
> > > >
> > > > After one day ,it still like this and no iteration has
> completed ,there
> > > is
> > > > also no error was turn up .There is no error in the input file
> because
> > I
> > > > have test it on anthoer computer which has 4 CPUs and it runs
> well .
> > > > I can't find the reason about this ,any help will be
> appreciated .
> > > > Best Regards
> > > > Q.J.Wang
> > > > XiangTan University
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL:
> > > >
> > >
> > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 3
> > > > Date: Sun, 6 Sep 2009 07:58:49 +0100
> > > > From: Bipul Rakshit <bipulrr at gmail.com>
> > > > Subject: Re: [Pw_forum] error loading shared libraries on
> parallel
> > > > execution
> > > > To: PWSCF Forum <pw_forum at pwscf.org>
> > > > Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com
> >
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > hi,
> > > > Just from root user type
> > > > yum install libgfortran.so.3
> > > >
> > > > then it will install this files which is not present in your
> machine
> > > >
> > > > On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti
> > > > <colonel.sreekar at gmail.com>wrote:
> > > >
> > > > > i know this issuehas been addressed and documented in
> troubleshooting
> > > > > section of the users guide.
> > > > > but i giveup in despair trying for a whole day to figure
> this problem
> > > > > i run my jobs on rocks cluster by using SGE's facility of
> submitting
> > > > batch
> > > > > jobs
> > > > >
> > > > >
> > > >
> > >
> > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html
> > > > >
> > > > > what i 'apparently' observe(or doubtfully infer) is that i can
> > > > successfully
> > > > > run a single parallel job, but on submitting a second job i
> get the
> > > error
> > > > > ____________________________________________
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > ____________________________________________
> > > > >
> > > > >
> > > > > i find out the path for the library and added to the
> LD_LIBRARY_PATH
> > by
> > > > > writing
> > > > > _______________________________________
> > > > > #set the library path to include gfortran libraries
> > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
> > > > >
> > > > >
> > > > > $ECHO
> > > > > $ECHO "$LD_LIBRARY_PATH"
> > > > > $ECHO
> > > > > _______________________________________
> > > > >
> > > > > in the file which acts as script for qsub ($qsub -pe orte 4
> > > > > dosroutine.qsub) which is
> > > > >
> > > > > dosroutine.qsub
> > > > >
> -----------------------------------------------------------------
> > > > >
> > > > > #!/bin/bash
> > > > > #
> > > > > #$ -cwd
> > > > > #$ -j y
> > > > > #$ -S /bin/bash
> > > > > #
> > > > >
> > > > > #extract the info about no of processors involved from
> command line
> > > > > arguments of 'qsub'
> > > > > PROCESSORS=$NSLOTS
> > > > >
> > > > > #heuristically assign the no of processors per pool NPR
> > > > > NPR=4
> > > > > #as a result no of pools are give by
> > > > > NPK=`expr $PROCESSORS / $NPR`
> > > > >
> > > > > #!/bin/bash
> > > > > #
> > > > > #
> > > > > #Script for performing a dos calculation on a parallel
> processor
> > > > > WORKINGDIR=`pwd`
> > > > > ECHO="echo"
> > > > >
> > > > > #set the library path to include gfortran libraries
> > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
> > > > >
> > > > >
> > > > > $ECHO
> > > > > $ECHO "$LD_LIBRARY_PATH"
> > > > > $ECHO
> > > > >
> > > > > # set the needed environment variables
> > > > >
> > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd`
> > > > > $ECHO $PREFIX
> > > > > BIN_DIR=$PREFIX/bin
> > > > > PSEUDO_DIR=$PREFIX/pseudo
> > > > > TMP_DIR=$HOME/tmp
> > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS"
> > > > > PARA_POSTFIX="-npool $NPK"
> > > > >
> > > > > # required executables and pseudopotentials
> > > > > $ECHO
> > > > > $ECHO " executables directory: $BIN_DIR"
> > > > > $ECHO " pseudo directory: $PSEUDO_DIR"
> > > > > $ECHO " temporary directory: $TMP_DIR"
> > > > >
> > > > > #create results directory
> > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do
> > > > > if test ! -d $DIR ; then
> > > > > mkdir $DIR
> > > > > fi
> > > > > done
> > > > > cd $WORKINGDIR/results
> > > > >
> > > > >
> > > > > # variables to represent programs
> > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
> > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
> > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x
> $PARA_POSTFIX"
> > > > >
> > > > >
> > > > > # DOS calculation for 0Ni0
> > > > > cat > 0ni0.dos.in << EOF
> > > > > &control
> > > > > calculation='nscf'
> > > > > restart_mode='from_scratch',
> > > > > prefix='0ni0',
> > > > > pseudo_dir = '$PSEUDO_DIR/',
> > > > > outdir='$TMP_DIR/'
> > > > > /
> > > > > &system
> > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,
> > > > > nspin = 2, starting_magnetization(1)=0.7,
> > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8,
> > > > > occupations='tetrahedra'
> > > > > /
> > > > > &electrons
> > > > > conv_thr = 1.0e-10
> > > > > mixing_beta = 0.7
> > > > > /
> > > > > ATOMIC_SPECIES
> > > > > Ni 58.69 NiUS.RRKJ3.UPF
> > > > > ATOMIC_POSITIONS
> > > > > Ni 0.0 0.0 0.0
> > > > > K_POINTS {automatic} !special points generated by
> tetrahedra
> > > > method
> > > > > 12 12 12 0 0 0
> > > > > EOF
> > > > >
> > > > > $ECHO " running DOS calculation for 0Ni0 ...\c"
> > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out
> > > > > $ECHO
> > > > > $ECHO " done"
> > > > >
> > > > > -------------------------------------------------------------
> > > > >
> > > > > the output i get is
> > > > >
> > > > > ************************************************
> > > > > :/usr/lib64:/usr/lib
> > > > >
> > > > > /home3/colonel/espresso-4.0.5
> > > > >
> > > > > executables directory: /home3/colonel/espresso-4.0.5/bin
> > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo
> > > > > temporary directory: /home3/colonel/tmp
> > > > > running DOS calculation for 0Ni0 ...\c
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading
> shared
> > > > > libraries: libgfortran.so.3: cannot open shared object file:
> No such
> > > > > file or directory
> > > > >
> > > > > done
> > > > > *************************************************
> > > > > plz suggest solutions which donot require root permissions ,
> as i
> > dont
> > > > have
> > > > > thanks in advance
> > > > > --
> > > > > Sreekar Guddeti
> > > > > Department of Physics
> > > > >
> > > > > _______________________________________________
> > > > > Pw_forum mailing list
> > > > > Pw_forum at pwscf.org
> > > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Dr. Bipul Rakshit
> > > > Research Associate,
> > > > S N Bose Centre for Basic Sciences,
> > > > Salt Lake,
> > > > Kolkata 700 098
> > > > India
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> > > > End of Pw_forum Digest, Vol 27, Issue 23
> > > > ****************************************
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> > >
> > >
> > >
> > > --
> > > Sreekar Guddeti
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> >
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> >
> > --
> > Sreekar Guddeti
> > -------------- next part --------------
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>
>
>
> --
> Sreekar Guddeti
> -------------- next part --------------
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---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
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