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@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)

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Message: 1 Date: Fri, 08 Apr 2011 17:21:02 +0800 From: Guoqiang PAN To: Matt Newville Cc: XAFS Analysis using Ifeffit , Bruce Ravel Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14) Message-ID: <1302254462.5791.25.camel@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

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@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 To: XAFS Analysis using Ifeffit Cc: Bruce Ravel Subject: [Ifeffit] Installation Artemis, athena in Fedora 14 Message-ID: <1302266514.10181.10.camel@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 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Installation Artemis, athena in Fedora 14 Message-ID: <201104080937.01794.bravel@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@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 To: gqpan@ustc.edu.cn Cc: XAFS Analysis using Ifeffit , Bruce Ravel Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14) Message-ID: 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 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

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@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

------------------------------

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