[Ifeffit] Ifeffit Digest, Vol 98, Issue 8
Guoqiang PAN
gqpan at ustc.edu.cn
Sun Apr 10 02:09:38 CDT 2011
I did as the Bruce's advice,
> 1. Check that Module::Build is indeed already on your system by
> typing this at the command line:
> perl -e "use Module::Build"
> If it responds with noting (i.e. no error messages), then you are
> fine.
>
> 2. Edit the files Bundle/LibPerlXrayBundle.pm and remove the line
> with Module::Build beneath the "CONTENTS" header.
>
> 3. Try again.
It's OK. Then to run ./build, it's easy to install artemis, athena and
hephaestus. Thank you and Matt very much.
Guoqiang
On Fri, 2011-04-08 at 12:00 -0500,
ifeffit-request at millenia.cars.aps.anl.gov wrote:
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> Today's Topics:
>
> 1. Re: Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14)
> (Guoqiang PAN)
> 2. Installation Artemis, athena in Fedora 14 (Guoqiang PAN)
> 3. Re: Installation Artemis, athena in Fedora 14 (Bruce Ravel)
> 4. Re: Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14)
> (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 08 Apr 2011 17:21:02 +0800
> From: Guoqiang PAN <gqpan at ustc.edu.cn>
> To: Matt Newville <newville at cars.uchicago.edu>
> Cc: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>,
> Bruce Ravel <bravel at bnl.gov>
> Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux
> (Fedora 14)
> Message-ID: <1302254462.5791.25.camel at localhost.localdomain>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks lot to Matt and Bruce.
> PGPLOT installation in Fedora 14 Linux case, can only be succeeded using
> g77_gcc_aout. I tried every possible choice for fortran-compiler in my
> case,only
> /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc_aout
> could work!
> Then PGPLOT_install script will use gfortran as default fortran
> compiler, it stopped at
>
> gfortran -c -O2 -fPIC grexec.f
> gfortran -c -O2 -fPIC /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f
> /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:208.72:
>
> & RECL=255, FORM='BINARY', IOSTAT=IER)
>
> 1
> Warning: FORM specifier in OPEN statement at (1) has invalid value
> 'BINARY'
> /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:240.72:
>
> & RECL=255, FORM='BINARY', IOSTAT=IER)
>
> 1
> Warning: FORM specifier in OPEN statement at (1) has invalid value
> 'BINARY'
> /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:654.21:
>
> BLKOUT(0) = 254
> 1
> Error: Arithmetic overflow converting INTEGER(4) to INTEGER(1) at (1).
> This check can be disabled with the option -fno-range-check
> make: *** [gidriv.o] Error 1
> gfortran -u -Wall -fPIC -O -o
> pgpack /usr/local/ifeffit-1.2.11c/pgplot/fonts/pgpack.f
> rm -f grfont.dat
> ./pgpack </usr/local/ifeffit-1.2.11c/pgplot/fonts/grfont.txt
> Characters defined: 996
> Array cells used: 26732
> rm -f pgpack
> gfortran -fno-backslash -o
> pgdemo1 /usr/local/ifeffit-1.2.11c/pgplot/examples/pgdemo1.f -L`pwd`
> -lpgplot_iff -lpng -lz -L/usr/X11R6/lib -lX11
> /usr/bin/ld: cannot find -lpgplot_iff
> collect2: ld returned 1 exit status
> make: *** [pgdemo1] Error 1
> = Cleaning up and preparing for test
> = = = = = = = = = = = = = = = = = = = = = = = = = =
> = Uh-oh. PGPLOT is missing some important files!
> = It looks like PGPLOT failed during building or
> = is only partially installed.
> =
> = Please consult the PGPLOT installation instructions
> = in the subdirectory pgplot/, and the log file:
> = /usr/local/ifeffit-1.2.11c/PGPLOT_install.log
> = which contains a full list of commands run.
> =
> = You may want to repeat these steps by hand or
> = consult the PGPLOT installations instructions
> = in install-unix.txt
>
>
> So if I commented out these two lines (line 219 and 220) in
> PGPLOT_install
> gfortran -v > /dev/null 2>&1
> if [ $? = 0 ] ; then fcompl='gfortran'; fi
> PGPLOT_install will be OK!
>
> As for installation ifeffit, I tried your suggestions
> e.g. (./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot
> -lpgplot_iff -lpng -lz -lX11') or ln -s libpgplot.a libpgplot_iff.a
> ,but not successful. It stopped at
>
> gcc -g -O2 -o ifftest1 ifftest1.o ../lib/libifeffit.a
> -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11
> -L/usr/lib/gcc/i686-redhat-linux/4.5.1
> -L/usr/lib/gcc/i686-redhat-linux/4.5.1/../../.. -lgfortran -lm -lgcc_s
> /usr/bin/ld: cannot find -lpgplot_iff
> collect2: ld returned 1 exit status
> make[3]: *** [ifftest1] Error 1
> make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c'
> make: *** [all-recursive-am] Error 2
> [root at localhost ifeffit-1.2.11c]#
>
> I think this also due to the gfortan, and I changed the fortran compiler
> to g77:
> ./configure --with-fortran=g77
> It is OK!
> Best regards,
> Guoqiang
>
>
> On Thu, 2011-04-07 at 11:56 -0500, Matt Newville wrote:
> > Guoqiang,
> >
> > Can we take a step back and try to figure out why PGPLOT_install
> > didn't work for you? It does work for me on Fedora14. What part of
> > PGPLOT_install did not work?
> >
> > It should be that ./configure --with-pgplot-link='LINKARGS' can be
> > used to specify the PGPLOT_LIBS value, say
> >
> > ./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot
> > -lpgplot_iff -lpng -lz -lX11'
> >
> > For PGPLOT installed with PGPLOT_install, or something like
> > ./configure --with-pgplot-link='-L/usr/local/pgplot -lpgplot -lpng
> > -lz -lX11'
> >
> > for a PGPLOT installed "by hand".
> >
> > An important difference between PGPLOT_install and most "by hand"
> > installations is that PGPLOT_install will not build a shared library,
> > but a static one only. This won't affect building, but can have an
> > impact for runtime, as the shared library needs to be found at
> > runtime, and so needs to be in the LD_LIBRARY_PATH, or configured with
> > ldconfig.
> >
> > --Matt
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 08 Apr 2011 20:41:54 +0800
> From: Guoqiang PAN <gqpan at ustc.edu.cn>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Cc: Bruce Ravel <bravel at bnl.gov>
> Subject: [Ifeffit] Installation Artemis, athena in Fedora 14
> Message-ID: <1302266514.10181.10.camel at localhost.localdomain>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,all
> Main trouble for the installation Artemis, athena etc. in PC Linux
> system (in my case is Fedora 14 ) is need to install all perl
> pre-requisites from CPAN. Following the install instruction I did as
> follows: perl -MCPAN -e 'install Bundle::XasPerlBundle'
> But it stopped at 'DAGOLDEN':
>
> Warning: Prerequisite 'Module::Metadata => 1.000002' for
> 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing
> 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'.
> Continuing, but chances to succeed are limited.
> Warning: Prerequisite 'CPAN::Meta => 2.110420' for
> 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing
> 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing,
> but chances to succeed are limited.
> Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for
> 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> suspicious. Skipping another build attempt, to prevent looping
> endlessly.
> Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for
> 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> suspicious. Skipping another build attempt, to prevent looping
> endlessly.
> Warning: Prerequisite 'version => 0.87' for
> 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> suspicious. Skipping another build attempt, to prevent looping
> endlessly.
> Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for
> 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> suspicious. Skipping another build attempt, to prevent looping
> endlessly.
> /usr/local/bin/perl Build --makefile_env_macros 1
> Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled
> lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/i686-linux /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm line 10.
> Compilation failed in require at lib/Module/Build/Base.pm line 23.
> BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23.
> Compilation failed in require at lib/Module/Build.pm line 15.
> BEGIN failed--compilation aborted at lib/Module/Build.pm line 15.
> Compilation failed in require at Build line 42.
> BEGIN failed--compilation aborted at Build line 42.
> make: *** [all] Error 2
> DAGOLDEN/Module-Build-0.3800.tar.gz
> /usr/bin/make -- NOT OK
> Warning (usually harmless): 'YAML' not installed, will not store
> persistent state
> Running make test
> Can't test without successful make
> Running make install
> Make had returned bad status, install seems impossible
>
> Guoqiang Pan
> National Synchrotron Radiation Laboratory
> University of Science & Technology of China
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 8 Apr 2011 09:37:01 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Installation Artemis, athena in Fedora 14
> Message-ID: <201104080937.01794.bravel at bnl.gov>
> Content-Type: Text/Plain; charset="utf-8"
>
>
> Guoqiang,
>
> Module::Build is the tool used to build and install my GUI software.
> It is a standard perl module and should already be on your system. I
> am surprised that your computer is finding it necessary to try to
> download and reinstall it.
>
> I assume that you are at the step of installing the things I call
> LibPerlXray and that you mis-typed.
>
> I suspect the fault is mine. I probably should not list Module::Build
> in the file Bundle/LibPerlXrayBundle.pm. Try the following:
>
> 1. Check that Module::Build is indeed already on your system by
> typing this at the command line:
> perl -e "use Module::Build"
> If it responds with noting (i.e. no error messages), then you are
> fine.
>
> 2. Edit the files Bundle/LibPerlXrayBundle.pm and remove the line
> with Module::Build beneath the "CONTENTS" header.
>
> 3. Try again.
>
> I apologize that this is so hard. I just don't have the resources to
> test these things on all possible systems, so I rely on the users to
> complain when they run into problems. Thanks for being patient.
>
> B
>
>
> On Friday, April 08, 2011 08:41:54 am Guoqiang PAN wrote:
> > Hi,all
> > Main trouble for the installation Artemis, athena etc. in PC Linux
> > system (in my case is Fedora 14 ) is need to install all perl
> > pre-requisites from CPAN. Following the install instruction I did as
> > follows: perl -MCPAN -e 'install Bundle::XasPerlBundle'
> > But it stopped at 'DAGOLDEN':
> >
> > Warning: Prerequisite 'Module::Metadata => 1.000002' for
> > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing
> > 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'.
> > Continuing, but chances to succeed are limited.
> > Warning: Prerequisite 'CPAN::Meta => 2.110420' for
> > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing
> > 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing,
> > but chances to succeed are limited.
> > Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for
> > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> > suspicious. Skipping another build attempt, to prevent looping
> > endlessly.
> > Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for
> > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> > suspicious. Skipping another build attempt, to prevent looping
> > endlessly.
> > Warning: Prerequisite 'version => 0.87' for
> > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> > suspicious. Skipping another build attempt, to prevent looping
> > endlessly.
> > Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for
> > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks
> > suspicious. Skipping another build attempt, to prevent looping
> > endlessly.
> > /usr/local/bin/perl Build --makefile_env_macros 1
> > Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled
> > lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1
> > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux
> > /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm
> > line 10. Compilation failed in require at lib/Module/Build/Base.pm line
> > 23. BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23.
> > Compilation failed in require at lib/Module/Build.pm line 15.
> > BEGIN failed--compilation aborted at lib/Module/Build.pm line 15.
> > Compilation failed in require at Build line 42.
> > BEGIN failed--compilation aborted at Build line 42.
> > make: *** [all] Error 2
> > DAGOLDEN/Module-Build-0.3800.tar.gz
> > /usr/bin/make -- NOT OK
> > Warning (usually harmless): 'YAML' not installed, will not store
> > persistent state
> > Running make test
> > Can't test without successful make
> > Running make install
> > Make had returned bad status, install seems impossible
> >
> > Guoqiang Pan
> > National Synchrotron Radiation Laboratory
> > University of Science & Technology of China
>
> --
>
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
>
> My homepage: http://xafs.org/BruceRavel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 8 Apr 2011 09:53:08 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: gqpan at ustc.edu.cn
> Cc: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>,
> Bruce Ravel <bravel at bnl.gov>
> Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux
> (Fedora 14)
> Message-ID: <BANLkTi=TERxR=UPKNfpdaybr6hsKtBFBrA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Guoqiang,
>
> Ah, I see and sorry for the trouble, especially I have had a fix (so
> that gfortran is used) for this for a while now. I believe you have
> a reasonable solution, but the PGPLOT_install script in the svn
> repository works better. I tried this on Fedora14 x86_64 yesterday
> revealed another problem, that I think I have fixed. I'll try to get
> that resolved and post a new PGPLOT_install script, and upload a
> ifeffit 1.2.11d tarball.
>
> Thanks
>
> --Matt
>
>
>
> On Fri, Apr 8, 2011 at 4:21 AM, Guoqiang PAN <gqpan at ustc.edu.cn> wrote:
> > Thanks lot to Matt and Bruce.
> > PGPLOT installation in Fedora 14 Linux case, can only be succeeded using
> > g77_gcc_aout. I tried every possible choice for fortran-compiler in my
> > case,only
> > /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc_aout
> > could work!
> > Then PGPLOT_install script will use gfortran as default fortran
> > compiler, it stopped at
> >
> > gfortran -c -O2 -fPIC grexec.f
> > gfortran -c -O2 -fPIC /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f
> > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:208.72:
> >
> > ? ? & ? ? ? ? RECL=255, FORM='BINARY', IOSTAT=IER)
> >
> > 1
> > Warning: FORM specifier in OPEN statement at (1) has invalid value
> > 'BINARY'
> > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:240.72:
> >
> > ? ? & ? ? ? ? ? ? ? RECL=255, FORM='BINARY', IOSTAT=IER)
> >
> > 1
> > Warning: FORM specifier in OPEN statement at (1) has invalid value
> > 'BINARY'
> > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:654.21:
> >
> > ? ? ? ? BLKOUT(0) = 254
> > ? ? ? ? ? ? ? ? ? ? 1
> > Error: Arithmetic overflow converting INTEGER(4) to INTEGER(1) at (1).
> > This check can be disabled with the option -fno-range-check
> > make: *** [gidriv.o] Error 1
> > gfortran -u -Wall -fPIC -O -o
> > pgpack /usr/local/ifeffit-1.2.11c/pgplot/fonts/pgpack.f
> > rm -f grfont.dat
> > ./pgpack </usr/local/ifeffit-1.2.11c/pgplot/fonts/grfont.txt
> > ?Characters defined: ? 996
> > ?Array cells used: ? 26732
> > rm -f pgpack
> > gfortran -fno-backslash -o
> > pgdemo1 /usr/local/ifeffit-1.2.11c/pgplot/examples/pgdemo1.f -L`pwd`
> > -lpgplot_iff -lpng -lz -L/usr/X11R6/lib -lX11
> > /usr/bin/ld: cannot find -lpgplot_iff
> > collect2: ld returned 1 exit status
> > make: *** [pgdemo1] Error 1
> > ?= Cleaning up and preparing for test
> > ?= = = = = = = = = = = = = = = = = = = = = = = = = =
> > ?= Uh-oh. ?PGPLOT is missing some important files!
> > ?= It looks like PGPLOT failed during building or
> > ?= is only partially installed.
> > ?=
> > ?= Please consult the PGPLOT installation instructions
> > ?= in the subdirectory ?pgplot/, and the log file:
> > ?= ? ?/usr/local/ifeffit-1.2.11c/PGPLOT_install.log
> > ?= which contains a full list of commands run.
> > ?=
> > ?= You may want to repeat these steps by hand or
> > ?= consult the PGPLOT installations instructions
> > ?= in install-unix.txt
> >
> >
> > So if I commented out these two lines ?(line 219 and 220) in
> > PGPLOT_install
> > ? ?gfortran -v > /dev/null 2>&1
> > ? ?if [ $? = 0 ] ; then ?fcompl='gfortran'; fi
> > PGPLOT_install will be OK!
> >
> > As for installation ifeffit, I tried your suggestions
> > e.g. (./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot
> > -lpgplot_iff -lpng -lz -lX11') or ln -s libpgplot.a libpgplot_iff.a
> > ,but not successful. It stopped at
> >
> > gcc ?-g -O2 ?-o ifftest1 ?ifftest1.o ../lib/libifeffit.a
> > -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11
> > -L/usr/lib/gcc/i686-redhat-linux/4.5.1
> > -L/usr/lib/gcc/i686-redhat-linux/4.5.1/../../.. -lgfortran -lm -lgcc_s
> > /usr/bin/ld: cannot find -lpgplot_iff
> > collect2: ld returned 1 exit status
> > make[3]: *** [ifftest1] Error 1
> > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test'
> > make[2]: *** [all-recursive] Error 1
> > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c'
> > make: *** [all-recursive-am] Error 2
> > [root at localhost ifeffit-1.2.11c]#
> >
> > I think this also due to the gfortan, and I changed the fortran compiler
> > to g77:
> > ./configure --with-fortran=g77
> > It is OK!
> > Best regards,
> > Guoqiang
> >
> >
> > On Thu, 2011-04-07 at 11:56 -0500, Matt Newville wrote:
> >> Guoqiang,
> >>
> >> Can we take a step back and try to figure out why PGPLOT_install
> >> didn't work for you? ?It does work for me on Fedora14. ? What part of
> >> PGPLOT_install did not work?
> >>
> >> It should be that ./configure --with-pgplot-link='LINKARGS' can be
> >> used to specify the PGPLOT_LIBS value, say
> >>
> >> ? ? ./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot
> >> -lpgplot_iff -lpng -lz -lX11'
> >>
> >> For PGPLOT installed with PGPLOT_install, or something like
> >> ? ? ./configure --with-pgplot-link='-L/usr/local/pgplot -lpgplot -lpng
> >> -lz -lX11'
> >>
> >> for a PGPLOT installed "by hand".
> >>
> >> An important difference between PGPLOT_install and most "by hand"
> >> installations is that PGPLOT_install will not build a shared library,
> >> but a static one only. ?This won't affect building, but can have an
> >> impact for runtime, as the shared library needs to be found at
> >> runtime, and so needs to be in the LD_LIBRARY_PATH, or configured with
> >> ldconfig.
> >>
> >> --Matt
> >
> >
> >
> >
>
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 98, Issue 8
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