sorry for making repeated posts but on <br>$./configure --enable-parallel --host=x86_64<br>configuration is successful for parallel version<br>on $make all<br> in the compilation report i get the following warnings related to libgfortran.so.3 and no other warnings <br>
<br>/usr/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, may conflict with libgfortran.so.3 ( 8 times)<br><br>/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)<br>
<br>hope this information is useful for suggesting a solution to the problem<br>sincerely,<br>sreekar guddeti<br>Dept.Physics<br>IIT Bombay<br>India<br><br><div class="gmail_quote">On Mon, Sep 7, 2009 at 6:36 AM, <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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When replying, please edit your Subject line so it is more specific<br>
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Today's Topics:<br>
<br>
1. Re: Pw_forum Digest, Vol 27, Issue 25 (sreekar guddeti)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 7 Sep 2009 06:36:10 +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 25<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:c864e4460909061806j5cde75efk76af1e8dba08d111@mail.gmail.com">c864e4460909061806j5cde75efk76af1e8dba08d111@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
> As an alternative, try static<br>
> link (add -static to LDFLAGS in make.sys).<br>
<br>
The other thing that i tried was<br>
$make clean<br>
$./configure --enable-parallel --disable-shared --host=x86_64<br>
<br>
output is<br>
___________________________________________<br>
configure: WARNING: If you wanted to set the --build type, don't use --host.<br>
If a cross compiler is detected then cross compile mode will be used.<br>
checking build system type... x86_64-unknown-linux-gnu<br>
configure: WARNING: incorrect host name ?<br>
checking architecture...<br>
configure: WARNING: unsupported architecture?<br>
checking for x86_64-g95... no<br>
checking for x86_64-gfortran... no<br>
checking for x86_64-f90... no<br>
checking for g95... no<br>
checking for gfortran... gfortran<br>
checking for Fortran 77 compiler default output file name... a.out<br>
checking whether the Fortran 77 compiler works... yes<br>
checking whether we are cross compiling... yes<br>
checking for suffix of executables...<br>
checking for suffix of object files... o<br>
checking whether we are using the GNU Fortran 77 compiler... yes<br>
checking whether gfortran accepts -g... yes<br>
checking for x86_64-mpif90... no<br>
checking for x86_64-gfortran... no<br>
checking for mpif90... mpif90<br>
checking whether we are using the GNU Fortran 77 compiler... yes<br>
checking whether mpif90 accepts -g... yes<br>
setting F90... gfortran<br>
setting MPIF90... mpif90<br>
checking for x86_64-cc... no<br>
checking for x86_64-gcc... no<br>
checking for cc... no<br>
checking for gcc... gcc<br>
checking whether we are using the GNU C compiler... yes<br>
checking whether gcc accepts -g... yes<br>
checking for gcc option to accept ANSI C... none needed<br>
setting CC... gcc<br>
checking how to run the C preprocessor... gcc -E<br>
checking for egrep... grep -E<br>
checking for ANSI C header files... yes<br>
checking for sys/types.h... yes<br>
checking for sys/stat.h... yes<br>
checking for stdlib.h... yes<br>
checking for string.h... yes<br>
checking for memory.h... yes<br>
checking for strings.h... yes<br>
checking for inttypes.h... yes<br>
checking for stdint.h... yes<br>
checking for unistd.h... yes<br>
checking for int *... yes<br>
checking size of int *... 8<br>
checking malloc.h usability... yes<br>
checking malloc.h presence... yes<br>
checking for malloc.h... yes<br>
checking for struct mallinfo.arena... yes<br>
checking for x86_64-gfortran... no<br>
checking for gfortran... gfortran<br>
checking whether we are using the GNU Fortran 77 compiler... yes<br>
checking whether gfortran accepts -g... yes<br>
setting F77... gfortran<br>
using F90... gfortran<br>
setting FFLAGS... -O3<br>
setting F90FLAGS... $(FFLAGS) -x f95-cpp-input<br>
setting FFLAGS_NOOPT... -O0<br>
setting CFLAGS... -O3<br>
setting CPP... cpp<br>
setting CPPFLAGS... -P -traditional<br>
setting LD... mpif90<br>
setting LDFLAGS... -static<br>
setting AR... ar<br>
setting ARFLAGS... ruv<br>
setting ARFLAGS_DYNAMIC...ruv<br>
checking whether make sets $(MAKE)... yes<br>
checking whether Fortran files must be preprocessed... no<br>
checking how to get verbose linking output from gfortran... -v<br>
checking for Fortran libraries of gfortran...<br>
-L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2<br>
-L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64 -L/lib/../lib64<br>
-L/usr/lib/../lib64 -L/opt/intel/Compiler/11.1/046/lib/intel64<br>
-L/opt/intel/Compiler/11.1/046/ipp/em64t/lib<br>
-L/opt/intel/Compiler/11.1/046/mkl/lib/em64t<br>
-L/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib<br>
-L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../.. -lgfortranbegin<br>
-lgfortran -lm -lgcc_s<br>
checking for dummy main to link with Fortran libraries... none<br>
checking for Fortran name-mangling scheme... lower case, underscore, no<br>
extra underscore<br>
checking for library containing dgemm... no<br>
in /usr/local/lib: checking for library containing dgemm... no<br>
in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing<br>
dgemm... no<br>
in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library<br>
containing dgemm... no<br>
in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library<br>
containing dgemm... no<br>
in<br>
/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:<br>
checking for library containing dgemm... no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm...<br>
no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm...<br>
no<br>
checking for library containing dgemm... no<br>
in /usr/local/lib: checking for library containing dgemm... no<br>
in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing<br>
dgemm... no<br>
in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library<br>
containing dgemm... no<br>
in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library<br>
containing dgemm... no<br>
in<br>
/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:<br>
checking for library containing dgemm... no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm...<br>
no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm...<br>
no<br>
checking for library containing zggev... no<br>
in /usr/local/lib: checking for library containing zggev... no<br>
in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing<br>
zggev... no<br>
in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library<br>
containing zggev... no<br>
in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library<br>
containing zggev... no<br>
in<br>
/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:<br>
checking for library containing zggev... no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing zggev...<br>
no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing zggev...<br>
no<br>
setting BLAS_LIBS... ../flib/blas.a<br>
setting LAPACK_LIBS... ../flib/lapack.a<br>
checking for library containing fftwnd... no<br>
in /usr/local/lib: checking for library containing fftwnd... no<br>
in /cineca/prod/gnu/lib: checking for library containing fftwnd... no<br>
in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing<br>
fftwnd... no<br>
in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library<br>
containing fftwnd... no<br>
in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library<br>
containing fftwnd... no<br>
in<br>
/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:<br>
checking for library containing fftwnd... no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing fftwnd...<br>
no<br>
in /opt/gridengine/lib/lx26-amd64: checking for library containing fftwnd...<br>
no<br>
setting FFT_LIBS...<br>
checking for library containing fftwnd... (cached) no<br>
setting MASS_LIBS...<br>
checking for library containing mpi_init... no<br>
setting MPI_LIBS...<br>
checking for library containing mpi_init... (cached) no<br>
setting DFLAGS... -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW<br>
setting IFLAGS... -I../include<br>
setting FDFLAGS... $(DFLAGS)<br>
setting RANLIB... echo<br>
configure: creating ./config.status<br>
config.status: creating include/fft_defs.h<br>
config.status: creating make.sys<br>
config.status: creating configure.msg<br>
config.status: creating include/c_defs.h<br>
config.status: include/c_defs.h is unchanged<br>
--------------------------------------------------------------------<br>
ESPRESSO can take advantage of several optimized numerical libraries<br>
(essl, fftw, mkl...). This configure script attempts to find them,<br>
but may fail if they have been installed in non-standard locations.<br>
If a required library is not found, the local copy will be compiled.<br>
<br>
The following libraries have been found:<br>
BLAS_LIBS=../flib/blas.a<br>
LAPACK_LIBS=../flib/lapack.a<br>
FFT_LIBS=<br>
Please check if this is what you expect.<br>
<br>
If any libraries are missing, you may specify a list of directories<br>
to search and retry, as follows:<br>
./configure LIBDIRS="list of directories, separated by spaces"<br>
<br>
Parallel environment not detected (is this a parallel machine?).<br>
Configured for compilation of serial executables.<br>
<br>
For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).<br>
--------------------------------------------------------------------<br>
configure: success<br>
______________________________________________<br>
<br>
but parallel version is not getting compiled<br>
<br>
<br>
sincerely,<br>
Sreekar Guddeti<br>
Dept. Physics<br>
IIT Bombay<br>
India<br>
<br>
<br>
<br>
<br>
On Mon, Sep 7, 2009 at 5:23 AM, <<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>
> You can reach the person managing the list at<br>
> <a href="mailto:pw_forum-owner@pwscf.org">pw_forum-owner@pwscf.org</a><br>
><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: Pw_forum Digest, Vol 27, Issue 24 (sreekar guddeti)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Mon, 7 Sep 2009 05:23:12 +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 24<br>
> To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
> Message-ID:<br>
> <<a href="mailto:c864e4460909061653j5cfaea62t9e77de6d42dba9da@mail.gmail.com">c864e4460909061653j5cfaea62t9e77de6d42dba9da@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> 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<br>
> -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW<br>
> -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<br>
> requires at runtime the shared libraries from the glibc version used for<br>
> 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<br>
> requires at runtime the shared libraries from the glibc version used for<br>
> linking<br>
> /opt/openmpi/lib/libopen-pal.a(if.o): In function `opal_ifaddrtoname':<br>
> (.text+0x780): warning: Using 'gethostbyname' in statically linked<br>
> applications requires at runtime the shared libraries from the glibc<br>
> version<br>
> used for linking<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> 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<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 144<br>
> in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> 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<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> 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<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 3916 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> 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<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 577 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> 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<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 378 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> 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<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 875 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> In function `free':<br>
> (.text+0x5f20): multiple definition of `free'<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first defined<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `free' changed from 256 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> In function `malloc':<br>
> (.text+0x4690): multiple definition of `malloc'<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first defined<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in<br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o)<br>
><br>
> /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o):<br>
> In function `realloc':<br>
> (.text+0x60f0): multiple definition of `realloc'<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first defined<br>
> here<br>
> /usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in<br>
> /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in<br>
> /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>
> On Sun, Sep 6, 2009 at 11:35 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>
> > You can reach the person managing the list at<br>
> > <a href="mailto:pw_forum-owner@pwscf.org">pw_forum-owner@pwscf.org</a><br>
> ><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: 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<br>
> running<br>
> > in 8 procs, but sometimes if the installation is not proper, it is<br>
> 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<br>
> has<br>
> > 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<br>
> > 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<br>
> > is<br>
> > > also no error was turn up .There is no error in the input file because<br>
> 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>
> > > <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>
> > -------------- next part --------------<br>
> > An HTML attachment was scrubbed...<br>
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> ><br>
> <a href="http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm" target="_blank">http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm</a><br>
> ><br>
> > ------------------------------<br>
> ><br>
> > 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<br>
> properties<br>
> > of pseudo potentials?<br>
> ><br>
> > *Fe.pbe-nd-rrkjus.UPF*<<br>
> > <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*<<br>
> > <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>
> ><br>
> > (*details* <<br>
> > <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>
> > -------------- next part --------------<br>
> > An HTML attachment was scrubbed...<br>
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> ><br>
> <a href="http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm" target="_blank">http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm</a><br>
> ><br>
> > ------------------------------<br>
> ><br>
> > 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<br>
> ,there<br>
> > > is<br>
> > > also no error was turn up .There is no error in the input file because<br>
> 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><<a href="http://people.sissa.it/%7Epaulatto/" target="_blank">http://people.sissa.it/%7Epaulatto/</a>><br>
> <<a href="http://people.sissa.it/%7Epaulatto/" target="_blank">http://people.sissa.it/%7Epaulatto/</a>><br>
> ><br>
> ><br>
> ><br>
> > ----------------------------------------------------------------<br>
> > SISSA Webmail <a href="https://webmail.sissa.it/" target="_blank">https://webmail.sissa.it/</a><br>
> > Powered by SquirrelMail <a href="http://www.squirrelmail.org/" target="_blank">http://www.squirrelmail.org/</a><br>
> ><br>
> ><br>
> ><br>
> > ------------------------------<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<br>
> and<br>
> > it is working fine(<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>
> ><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>
> > > You can reach the person managing the list at<br>
> > > <a href="mailto:pw_forum-owner@pwscf.org">pw_forum-owner@pwscf.org</a><br>
> > ><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>
> > ><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<br>
> > 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<br>
> 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<br>
> 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>
> > > -------------- next part --------------<br>
> > > An HTML attachment was scrubbed...<br>
> > > URL:<br>
> > ><br>
> ><br>
> <a href="http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm" target="_blank">http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm</a><br>
> > ><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>
> > > <<br>
> <a href="mailto:25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com">25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com</a><br>
> > ><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<br>
> 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<br>
> 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<br>
> > is<br>
> > > also no error was turn up .There is no error in the input file because<br>
> 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>
> > > -------------- next part --------------<br>
> > > An HTML attachment was scrubbed...<br>
> > > URL:<br>
> > ><br>
> ><br>
> <a href="http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm" target="_blank">http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm</a><br>
> > ><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>
> > ><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<br>
> > 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<br>
> 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<br>
> 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>
> > > -------------- next part --------------<br>
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> > ><br>
> > > ------------------------------<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>
> > > End of Pw_forum Digest, Vol 27, Issue 23<br>
> > > ****************************************<br>
> > ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > Sreekar Guddeti<br>
> > -------------- next part --------------<br>
> > An HTML attachment was scrubbed...<br>
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> ><br>
> > ------------------------------<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>
> > End of Pw_forum Digest, Vol 27, Issue 24<br>
> > ****************************************<br>
> ><br>
><br>
><br>
><br>
> --<br>
> Sreekar Guddeti<br>
> -------------- next part --------------<br>
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><br>
> ------------------------------<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>
> End of Pw_forum Digest, Vol 27, Issue 25<br>
> ****************************************<br>
><br>
<br>
<br>
<br>
--<br>
Sreekar Guddeti<br>
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<br>
------------------------------<br>
<br>
_______________________________________________<br>
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<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
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<br>
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End of Pw_forum Digest, Vol 27, Issue 26<br>
****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Sreekar Guddeti<br><br>