Re: Install on Susev11

[James Quirk]

Nick,

You should try doing the following manual build.

(i) Add the following to your .bashrc file:

eval `/home/np/AMRITA/AMRITAv3.04/tools/amrshell -setup bash`

then open up a new shell and check that the command has taken e.g.:

echo $AMRITA

(ii) Run the following command:

amrmake -verbose amrita

and post the output here.

As far as I'm aware AMRITA has not been installed on an OpenSUSE 11.2
machine and so it's possible that there is a glitch or two that will
need to ironed out before the installation will work seamlessly.
There's also a possibility that your setup is not quite right.
Either way the output obtained with -verbose should shed light on the
problem.

James

On Thu, 10 Dec 2009, Nicholaus Parziale wrote:

> Dr. Quirk,
>
> I am attempting to install AMRITA on my machine:
>
> OS: Linux 2.6.31.5-01-desktop x86_64
> System: openSUSE 11.2(x86_64)
> KDE: 4.3.1 (KDE 4.3.1) "release 6"
>
> The install of openSUSE was new.
>
> I have installed make, and all the packages that
>
> perl AMRITAv3.04_R07-12-2009 -build Linux/x86_64
>
>
> call for (gcc-fortran,gcc-++ ect)
>
>
> the install fails as below:
>
> ***************************
>
> installation kit is
> intact!
> ***************************
>
> ******************
>
> amrita
> flightcheck
> ******************
>
> passed
> flightcheck!
> keeping record:
> $AMRITA/logs/target/serial/Linux/x86_64/O/src3p::perl
> ********************
>
> amrbuild
> src3p::perl
> ********************
>
> ******************************************************
>
> amrbuild missing:
> /home/np/AMRITA/AMRITAv3.04/bin/perl
> ******************************************************
>
> ********************************
>
> amrbuild failed for
> src3p::perl!
> ********************************
>
> keeping record:
> $AMRITA/logs/target/serial/Linux/x86_64/O/src3p::mpeg
> ********************
>
> amrbuild
> src3p::mpeg
> ********************
>
> building codec
> amrcc: error: AMRITA::system -- command not found!
> error near: end of line
> building huffman
> amrcc: error: AMRITA::system -- command not found!
> error near: end of line
> building io
> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/src3p::origami
> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/plugin::amrita
> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/plugin::amr_sol
> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/plugin::foo
> ^C
>
> ***************************************
> failed to build AMRITAv3.04_R07-12-2009
> ***************************************
> src3p::perl failed!
> src3p::mpeg uknown
> src3p::origami uknown
> plugin::amrita uknown
> plugin::amr_sol uknown
> plugin::foo uknown
> amrmake:
> Consult Chapter 3 of Amrita's installation notes and try again.
> ********************************************
> The automatic build 'amrmake amrita' failed.
> You will need to build AMRITA manually.
> ********************************************
>
> Is there another package I need to install?/
>
> Take care,
>
> Nick Parziale
>
>

[James Quirk]

Nick,
>
> Continue? [yes] >>yes

> keeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/src3p::perl
> ********************
> amrbuild src3p::perl
> ********************

This build is failing because there is an incompatibility between
the Perl shipped wiith OpenSUSE 11.2 and the Perl modules shipped
with AMRITA. However, if you can run:

amrperl

and get the response:

Usage: amrperl [options] file

--amrperl-help display this help message
--amrperl-debug turn base-level debugging on
--amrperl-debug1 display how Perl will be activated and exit

etc.

then you can ignore this problem for now.

> ********************
> amrbuild
> src3p::mpeg
> ********************

This build is failing because it is using:
>
> AMRITA::system { verbose
> mode
>
> gcc-4.2 -O3 -w -m32 -fPIC -I/usr/X11R6/include -I/usr/include
> \
> -I/home/np/AMRITA/AMRITAv3.04/include/cc
> -I/home/np/AMRITA/AMRITAv3.04/src
> \
> -I/include/cc -I. -I.. -I/include/ -Dserial_code -DLinux_x86_64 -D_code
> -c \
>
> ./codec.c

>
> }
>
> amrcc: error: AMRITA::system -- command not
> found!

and you likely do not have gcc-4.2 installed on your machine.

If you take a look at the file:

$AMRITA/SYSTEM/Linux/x86_64/which-gcc

you'll see it is set up to switch between gcc-4.3 and gcc-4.2
depending on the word size. This is needed on OpenSUSE 10.x and 11.1
because the default gcc, 4.3, can't handle the 32-bit compilation
needed by src3p::mpeg and src3p::origami.

I'm not sure what gcc is the default on OpenSUSE 11.2, but it may
well be 4.4 in which case the 32-bit compilation problem might be fixed.
But in any case you should tune the contents of which-gcc to match
your local set up.
>
> ***********************
> amrbuild
> src3p::origami
> ***********************
This build is failing for the same reasons as src3p::mpeg.

> amrcc: error: AMRITA::system -- command not found!
> error near: end of line

> building fieldedt.C

> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/plugin::amrita
> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/plugin::amr_sol

> ************************
> amrbuild plugin::amr_sol
> ************************
> building
> /home/np/AMRITA/AMRITAv3.04/obj/serial/Linux/x86_64/O/amr_sol/expr_mgr.o
> ^Ckeeping record: $AMRITA/logs/target/serial/Linux/x86_64/O/plugin::foo
Here your log file seems to be corrupted, or at least it is missing
information I would expected to see. Can you send me the output of:

amrmake -force -verbose plugin::amrita

so that I can diagnose the problem further.

James

[James Quirk]

Nick,

On Fri, 11 Dec 2009, Nicholaus Parziale wrote:

> Dr. Quirk, All,
>
> I dont NOT have gcc-4.2 I have gcc-4.4 . gcc-4.3 is available via the
> download. Would this suffice? Or do I need to install gcc-4.2 ? Or do I need
> to install both?
No. Edit your which-gcc file so that it selects gcc-4.4 so will look like:

$g77 = 'gfortran-4.4';
$gcc = 'gcc-4.4';
$gxx = 'g++-4.4';
$g2c = 'gfortran';
if($word eq '32') {
$gcc = 'gcc-4.4';
}

> np@linux-lgcr:~>
> amrperl
>
> Usage: amrperl [options]
> file
Your amrperl is working so you can ignore the src3p::perl for now.
>
> You have requested:
>
> ***********************
> amrbuild plugin::amrita
> ***********************
> building
> /home/np/AMRITA/AMRITAv3.04/obj/serial/Linux/x86_64/O/amrita/isl_parser.o
This failed as your which-gcc was selecting gcc-4.3 which you don't have.
But when you change it to gcc-4.4 you should be able to run:

amrmake -force amrita

If all goes well:

plugin::amrita
plugin::amr_sol
plugin::foo

should all build. src3::perl will be broken and src3p::{mpeg,origami}
may or may not build depending on whether gcc-4.4 has fixed the bug
in gcc-4.3 that prevents it from building 32-bit executables.

James

[James Quirk]

Nick,
>
> I have Googled "which-gcc" and downloaded locate to find "which-gcc" . I
> cannot find it. What is it and how can I find it?
>
I did actually explain the location and purpose of which-gcc in
one of my previous e-mails to you. I'm attaching the relevant
portion of the message below.

James

[James Quirk]

> I have Googled "which-gcc" and downloaded locate to find "which-gcc" . I
> cannot find it. What is it and how can I find it?

If you'd searched for:

which-gcc amrita

you would have found a posting to this newsgroup dated Nov 29.

[James Quirk]

Nick,

>
> building
> codec

> amrcc: error: AMRITA::system -- command

This suggests that you have not edited the which-gcc file correctly.
In any event, without the -verbose option there is not enough
information to advise you.

James

[James Quirk]

Nick,

> ********************************
> finished building plugin::amrita
> ********************************
> Sanity Checks
> libamrita OK!
> libamrita_gl OK!
> plugin::amrita OK!
> **************************************************************
> installed plugin::amrita in: $AMRITA/bin/serial/Linux/x86_64/O
> **************************************************************
OK. That looks good.

Now you need to run:

amrmake -force plugin::amr_sol

and if that compiles okm you should try running the example obtaine with:

amrcp Chp2/my.script

James

[James Quirk]

Nick,

> ***************************************************************
> installed plugin::amr_sol in:
> $AMRITA/bin/serial/Linux/x86_64/O
> ***************************************************************
>
Yes, it looks like you're in good shape.

> np@linux-xzir:~/AMRITA/AMRITAv3.04> amrcp
You do not want to issue amrcp from within AMRITA's tree structure.
Nor should you run an AMRITA script from within the tree. To do so
runs the risk of corrupting your installation. The idea is that
you run scripts elsewhere as in:

cd
mkdir TEST
cd TEST
amrcp Chp2/my.script
amrita my.script
amrview ps/schlieren.ps
amrview ps/grid.ps

that was the TEST directory can safely be deleted without
impacting on the core installation.

>
> Is there any next step or is the installation complete?
We still need to figure out how to build src3p::origami
with gcc-4.4 . What does your which-gcc file now look like?
And what is the outcome of:

amrmake -verbose src3p::origami

James

p.s. If the build gives you lots of errors, jut post a
representative sample.

[James Quirk]

Nick,

> \
> /usr/include/gnu/stubs.h:7:27: error: gnu/stubs-32.h: No such file or
> directory
> }
>
You will need to install the OpenSUSE 11.2 RPMs that provide 32bit
support when compiling under x86_64. I think they are:

glibc-devel-32bit-2.10.1-10.x86_64.rpm
gcc44-32bit-4.4.1_20090817-2.3.4.x86_64.rpm
libgcc44-4.4.1_20090817-2.3.4.x86_64.rpm

James

[James Quirk]

>
> glibc-devel-32bit-2.10.1-10.x86_64.rpm
> gcc44-32bit-4.4.1_20090817-2.3.4.x86_64.rpm
> libgcc44-4.4.1_20090817-2.3.4.x86_64.rpm
That last RPM should have been:

libgcc44-32bit-4.4.1_20090817-2.3.4.x86_64.rpm

and all three are available from:

http://www.rpmfind.net/linux/RPM/openSUSE_11.2.html

James

[James Quirk]

Nick,

src3p::origami has compiled OK but the linking has failed:

> when searching for -lXm \
>
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: \
> skipping incompatible /usr/lib64/libXm.so when searching for -lXm \
>
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: \
> cannot find -lXm collect2: ld returned 1 exit status
>
> }
because you're linking a 32bit executable against 64bit libaries.
I don't have time this evening to sort out what needs to be done,
but I will take a look at it tomorrow.

James