Error when running make install

ASand

Hi,

I encountered the error below when I ran make install:

/usr/bin/mkdir -p '/home/anjali.sandip/issm-project/trunk-jpl/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c issm.exe issm_slc.exe kriging.exe '/home/anjali.sandip/issm-project/trunk-jpl/bin'
libtool: install: /usr/bin/install -c .libs/issm.exe /home/anjali.sandip/issm-project/trunk-jpl/bin/issm.exe
/usr/bin/install: cannot stat '.libs/issm.exe': No such file or directory
make[3]: *** [Makefile:2816: install-binPROGRAMS] Error 1
make[3]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/c'
make[2]: *** [Makefile:9610: install-am] Error 2
make[2]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/c'
make[1]: *** [Makefile:471: install-recursive] Error 1
make[1]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
make: *** [Makefile:592: install-recursive] Error 1

Any help would be much appreciated,
Anjali

justinquinn

ASand Hi Anjali, could you please attach or copy/paste your configuration?

ASand

configure.sh

884B

justinquinn

ASand Can you please do make 2>&1 | tee make.log and attach the log here?

ASand

Here is the log:
make all-recursive
make[1]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl'
Making all in src
make[2]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
Making all in c
make[3]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src/c'
CXXLD issm.exe
CXXLD issm_slc.exe
CXXLD kriging.exe
make[3]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/c'
Making all in m
make[3]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src/m'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/m'
Making all in wrappers
make[3]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src/wrappers'
make[4]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src/wrappers'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/wrappers'
make[3]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/wrappers'
make[3]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
make[2]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
make[2]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl'
make[2]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl'
make[1]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl'

justinquinn

ASand Okay, that looks good. Could you please try make install again?

ASand

I did. I am running into the same error.

justinquinn

ASand Could you please try autoreconf -ivf; make; make install?

ASand

I tried. Still the same error...

justinquinn

ASand If you run echo $ISSM_DIR, do you get /home/anjali.sandip/issm-project/trunk-jpl? If that's correct, I think the issue may be the . in your user name.

As an aside, which version of autotools are your using?

ASand

Yes, I get

/home/anjali.sandip/issm-project/trunk-jpl

The version is 2.69.

How do you suggest I proceed?

justinquinn

ASand I'm really stumped. Is this your own machine? Do you have the ability to create a new user account without a . in the name? I only bring it up because, although Linux allows it, I could see how it might create issues when running certain commands.

As well, I just noticed trunk-jpl in your $ISSM_DIR, implying this is a copy of the developers svn repo. we have moved to GitHub, so I recommend checking out a new copy anyhow: https://github.com/ISSMteam/ISSM

ASand

I reinstalled ISSM from the GitHub link you provided. I now encounter this error when I run make

./bamg/././././././../shared/./Exceptions/../io/Comm/../../../toolkits/mpi/issmmpi.h:63:26: fatal error: mpi.h: No such file or directory
63 | #include <mpi.h>
| ~_~~
compilation terminated.

justinquinn

ASand Do you have mpi.h in $ISSM_DIR/externalpackages/petsc/install/include? If so, you just need to run source $ISSM_DIR/etc/environment.sh and run make again.

ASand

Please disregard my previous comment. I was able to resolve it. Here is the error I encounter when I run make:

/usr/bin/ld: /home/anjali.sandip/ISSM/ISSM/externalpackages/m1qn3/install/libm1qn3.so: relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:4723: libISSMCore.la] Error 1
make[3]: Leaving directory '/home/anjali.sandip/ISSM/ISSM/src/c'
make[2]: *** [Makefile:470: all-recursive] Error 1
make[2]: Leaving directory '/home/anjali.sandip/ISSM/ISSM/src'
make[1]: *** [Makefile:525: all-recursive] Error 1
make[1]: Leaving directory '/home/anjali.sandip/ISSM/ISSM'
make: *** [Makefile:457: all] Error 2

mathieumorlighem

recompile with -fPIC

Hi Anjali you need to reinstall m1qn3. I don't know which script you are using but take a look at it and make sure it includes -fPIC

ASand

Does this look right?

Compile and install

if which mpifort 2>/dev/null; then
export FC="mpifort"
else
	if which ifort 2>/dev/null; then
		export FC="ifort"
		export FFLAGS="-traceback -check all -fPIC" # -O2 is default
	else
		export FC="gfortran"
		if [ `uname` == "Darwin" ]; then
			FFLAGS="-arch $(uname -m)"
		else
			FFLAGS=""
		fi
		export FFLAGS
	fi
fi

mathieumorlighem

You may need to add

export FFLAGS="-fPIC"

above this, give it a try!

ASand

Thank you. That seems to have fixed it, but now I encounter a new error when I run make:

configure.sh

825B

/usr/bin/ld: ./.libs/libISSMCore.so: undefined reference to symbol 'gfortran_transfer_real_write@@GFORTRAN_8'
/usr/bin/ld: /usr/lib64/libgfortran.so.5: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:5075: issm.exe] Error 1
make[3]: *** Waiting for unfinished jobs....
/usr/bin/ld: /usr/bin/ld: ./.libs/libISSMCore.so./.libs/libISSMCore.so: undefined reference to symbol ': undefined reference to symbol 'gfortran_transfer_real_write@@GFORTRAN_8_gfortran_transfer_real_write@@GFORTRAN_8''

/usr/bin/ld/usr/bin/ld: : /usr/lib64/libgfortran.so.5/usr/lib64/libgfortran.so.5: error adding symbols: : error adding symbols: DSO missing from command lineDSO missing from command line

collect2: error: ld returned 1 exit status
collect2: error: ld returned 1 exit status

I have attached the configure.sh for reference. Thank you for any suggestions you can provide.

mathieumorlighem

Do you have --with-fortran-lib in your configure.sh script? I think you need something like

--with-fortran-lib="-L/usr/lib64/ -lgfortran