Re: [Apbs-users] APBS-1.1.0 configure with ACML 4.2.0 BLAS - error: BLAS libraries or headers missing

[Greg G. <gg...@gm...>]

Thanks Mark, it's good to know when the flags take effect.

Nathan, I think overwrote the config.log.

In the meantime I've been screwing around.

./setup.sh ( blindly following the iAPBS/NAMD install.sh and forgot
this last time )

./configure --with-blas="-L/opt/acml4.2.0/gfortran64/lib -static
-lacml" --with-blas-name=acml

Configured successfully ( even though the ACML BLAS library is
libacml[a.so] but apparently "The only difference between using an -l
option and specifying a file name is that -l surrounds library with
`lib' and `.a' and searches several directories.") to:

but make failed with:

gfortran -g -O2 -DVAPBSQUIET -o apbs main.o
/n/home/gguthe/apbs-1.1.0-source/bin/.libs/libapbsmainroutines.a
/n/home/gguthe/apbs-1.1.0-source/src/aaa_lib/.libs/libapbs.a
-L/n/home/gguthe/apbs-1.1.0-source/contrib/lib
/n/home/gguthe/apbs-1.1.0-source/contrib/lib//libmaloc.a -lm
-L/opt/acml4.2.0/gfortran64/lib -lacml
/usr/bin/ld: warning: libgfortran.so.3, needed by
/opt/acml4.2.0/gfortran64/lib/libacml.so, not found (try using -rpath
or -rpath-link)
/usr/bin/ld: warning: libgomp.so.1, needed by
/opt/acml4.2.0/gfortran64_mp/lib/libacml_mv.so, not found (try using
-rpath or -rpath-link)
/opt/acml4.2.0/gfortran64/lib/libacml.so: undefined reference to
`_gfortran_string_index@GFORTRAN_1.0'
/opt/acml4.2.0/gfortran64/lib/libacml.so: undefined reference to
`_gfortran_st_write_done@GFORTRAN_1.0'
/opt/acml4.2.0/gfortran64/lib/libacml.so: undefined reference to
`_gfortran_st_read_done@GFORTRAN_1.0'
...
collect2: ld returned 1 exit status
make[1]: *** [apbs] Error 1
make[1]: Leaving directory `/home/nfs/users/gguthe/apbs-1.1.0-source/bin'
make: *** [all-recursive] Error 1

Same result after adding --with-gnu-ld and setting
LD_LIBRARY_PATH=/n/app/openmpi-1.2/lib:/opt/acml4.2.0/gfortran64_mp/lib:/opt/acml4.2.0/gfortran64/lib

It kept trying to link libacml.so despite the -static in --with-blas, so:

./configure --with-blas=/opt/acml4.2.0/gfortran64/lib/libacml.a

which configured and make installed cleanly, but failed the tests.

iAPBS installed with the same configuration, but I couldn't make it
against NAMD (after removing the flags -llapack from the
namd2/arch/Linux-x86_64.apbs file)

:/n/home/<myhome>/apbs-1.1.0-source/contrib/pmgZ/mlinpckd.f:522:
undefined reference to `_gfortran_st_write_done'
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /n/home/gguthe/namd2/Linux-x86_64-MPI

Anyway, linker problems probably time to RTF gcc and ld manuals and
stop randomly flailing about.

Greg

On Wed, Jun 10, 2009 at 9:37 PM, Mark Abraham<mar...@an...> wrote:
>
>
> On 06/11/09, Greg Guthe <gg...@gm...> wrote:
>
> Hi,
>
> I'm trying to build APBS-1.1.0 with the BLAS from ACML 4.2.0 for our
> Linux Opteron cluster:
>
> $ ./configure --with-blas="-L/opt/acml4.2.0/gfortran64/lib
> -I/opt/acml4.2.0/gfortran64/include -lacml -lgfortran"
> --with-blas-name=libacml
>
> IIRC, --with-blas is intended for link-time flags, whereas -I is a
> compile-time flag, which you need to supply (for example) with ./configure
> CFLAGS="-I/path/to/blas/include" --with-blas="-L/path/to/blas/lib -lacml"
> --with-blas-name=libacml
>
>  Mark
>
> ...
> checking for --with-blas... -L/opt/acml4.2.0/gfortran64/lib
> -I/opt/acml4.2.0/gfortran64/include -lacml -lgfortran
> configure: checking libacml using -L/opt/acml4.2.0/gfortran64/lib
> -I/opt/acml4.2.0/gfortran64/include -lacml -lgfortran
> checking for dscal in -llibacml... no
> configure: error: BLAS libraries or headers missing:  exiting on error!
>
> ... and it's not working. Tried blas names libacml.a libacml.so
> libacml_mv.a libacml_mv.so, adding -static and dropping -lgfortran
> from blas flags.
>
> Anywho,
> Greg
>
> http://developer.amd.com/documentation/htmlhelp/acml/pages/GeneralInformation.aspx#linking_002flinux
>
> http://apbs.wustl.edu/MediaWiki/index.php/Installation_and_availability#Using_an_external_BLAS_library
> http://sourceforge.net/mailarchive/message.php?msg_id=20060919225949.GA24351%40ucsd.edu
> http://sourceforge.net/mailarchive/message.php?msg_id=4e7688580609191604q5114b67s74c6109e751cf411%40mail.gmail.com
>
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