Installation in RedHat 8, stuck at Silo

[zl]

To whom it may concern,

     I hope you are having a great weekend!

     I am trying to install IBAMR 0.8.0 in RedHat 8. It got stuck in the installation of Silo. I tried to install it along with PETSc

/configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --with-debugging=1 --download-hypre=1 --download-fblaslapack --with-x=0 --download-silo=../silo-4.10-bsd-smalltest.tgz --download-hdf5=1

      But, an error message comes up while configuring (please see the attached configure.log for more details)

      Then, I tried to install a standalone version by

./configure CC=gcc CXX=g++ FC=gfortran F77=gfortran --prefix=$HOME/sfw/linux/silo/4.10 --disable-silex --with-zlib="/usr/local/zlib/include,/usr/local/zlib/lib"

      The configuring succeeds, but "make -j16" encounters a problem:

mv -f .deps/silock.Tpo .deps/silock.Po

/bin/sh ../../libtool --tag=CXX   --mode=link g++  -fPIC  -L/usr/local/zlib/lib -L/usr/gapps/silo/szip/2.1/i386-pc-linux-gcc-3.2.3/lib -L/usr/gapps/silo/hdf5/1.6.6/i386-pc-linux-gcc-3.2.3/lib -o silock silock.o ../../src/libsilo.la  -lz  -lz -lm -lsz

libtool: link: g++ -fPIC -o silock silock.o  -L/usr/local/zlib/lib -L/usr/gapps/silo/szip/2.1/i386-pc-linux-gcc-3.2.3/lib -L/usr/gapps/silo/hdf5/1.6.6/i386-pc-linux-gcc-3.2.3/lib ../../src/.libs/libsilo.a -lz -lm -lsz

/usr/bin/ld: cannot find -lsz

collect2: error: ld returned 1 exit status

make[3]: *** [Makefile:404: silock] Error 1

make[3]: Leaving directory '/home/wei_lab/sfw/linux/silo-4.10/tools/silock'

make[2]: *** [Makefile:387: all-recursive] Error 1

make[2]: Leaving directory '/home/wei_lab/sfw/linux/silo-4.10/tools'

make[1]: *** [Makefile:437: all-recursive] Error 1

make[1]: Leaving directory '/home/wei_lab/sfw/linux/silo-4.10'

      I googled a little and can not find how to handle the "cannot find -lsz" issue. 

Could you please kindly provide some help?

thanks,

zl

     

[Boyce Griffith]

It looks like Amneet already replied, but a separate issue is that it seems like you are using a very old version of GCC (3.3.2). You will need to use a more recent compiler to use IBAMR and libMesh since both use C++11. I think that everything will work with GCC 4.8.1, which is itself quite old, although I would suggest using a more recent version.

On Mar 28, 2021, at 4:52 PM, zl <alan.wei...@gmail.com> wrote:

To whom it may concern,

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[alan.wei...@gmail.com]

Good morning Dr. Griffith,

     Thanks for pointing that out. Just wondering did you find that I am using GCC(3.3.2) from

 

/bin/sh ../../libtool --tag=CXX   --mode=link g++  -fPIC  -L/usr/local/zlib/lib -L/usr/gapps/silo/szip/2.1/i386-pc-linux-gcc-3.2.3/lib -L/usr/gapps/silo/hdf5/1.6.6/i386-pc-linux-gcc-3.2.3/lib -o silock silock.o ../../src/libsilo.la  -lz  -lz -lm -lsz

 

     It is interesting as when I check my gcc’s version by typing “gcc –version”, this is what I found:

 

gcc (GCC) 8.3.1 20191121 (Red Hat 8.3.1-5)

Copyright (C) 2018 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

 

     Not sure why silo configure use -L/usr/gapps/silo/szip/2.1/i386-pc-linux-gcc-3.2.3/lib.

     Any thoughts or it does not matter?

 

Thanks again

Alan

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