Hello again,

I am having issues with spatialindex on my RHEL HPC machine (-no_package_manager). I installed spatialindex 1.8.5 from source (w/ prefix=$HOME/.local) and added $HOME/.local/include and $HOME/.local/lib to $CPATH and $LD_LIBRARY_PATH respectively. But I am getting this error:

g++ -pthread -shared build/temp.linux-x86_64-2.7/firedrake/spatialindex.o -lspatialindex -o /turquoise/users/jychang48/firedrake-deps/firedrake/src/firedrake/firedrake/spatialindex.so
/usr/bin/ld: cannot find -lspatialindex
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1

I did"mpicc -x c -v -E /dev/null" and saw that /users/jychang48/.local/include is there, but when I look at LIBRARY_PATH, /users/jychang48/.local/lib is not there.

How can I fix this?

Thanks,

Justin

On Fri, Oct 30, 2015 at 4:16 AM, David Ham <David.Ham@imperial.ac.uk> wrote:

Thanks for catching this, Justin. Miklos has made a fix to the install script accordingly.

Cheers,

David

On Thu, 29 Oct 2015 at 19:33 Justin Chang <jychang48@gmail.com> wrote:

Hi Lawrence,

Yeah the issue was that /usr/local/include was not shown originally. I ran code-select --install and everything runs fine now.

Thanks,

Justin

On Thu, Oct 29, 2015 at 3:21 AM, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> wrote:

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 29/10/15 07:45, Justin Chang wrote:
> I just did a fresh install on my Macbook (also upgraded to El
> Capitan) but I am still getting errors. Attached is the log file.
>
> Can you guys tell what's going on?

firedrake/spatialindex.cpp:259:10: fatal error:
'spatialindex/SpatialIndex.h' file not found
#include "spatialindex/SpatialIndex.h"

Suggests that although spatialindex appears to be installed, your
compiler does not find it. This header file should be in
/usr/local/include

So what do the following say?

$ ls /usr/local/include/spatialindex
$ mpicc -x c -v -E /dev/null

The latter should print out a section:

#include <...> search starts here:
LIST OF DIRECTORIES
End of search list

If /usr/local/include doesn't appear in this list of directories can
you try:

$ xcode-select --install

And then check again.

Cheers,

Lawrence
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.22 (GNU/Linux)

iQEcBAEBAgAGBQJWMeU2AAoJECOc1kQ8PEYv6lUH/R1JnxVnmIDheeqQ4Z0xWuSq
ePznzKtGb4cQPRddBxksC46miENCdeXF3zhOEAfqGV5eaAum/7xW7FgzbiPHy+dl
9V1RyKnzQm+WXHS0dfWuqa0QOJITnJivzyMZxm7Rt5Ayqa/S5AK2yq2fsI399JI8
Nwt53/yFjRvy/pja7YhCTMfb/gquz82ZP/EvtU5RWcHEh+Fr1MQ///GzJVRDGgGk
ldSxdawDJW8sAdmUkdtLmwEj1tfRXRVtrdKg0fzgFWjEzhFbzOH8lUNavoKsLJHu
SpIjFvc1BEbR67hzsJugeRN9ZWNJhwLn1X5Hu1CIhYfM+IR0kx9SnkJKMYHjc3I=
=0S8+
-----END PGP SIGNATURE-----

_______________________________________________
firedrake mailing list
firedrake@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake

_______________________________________________
firedrake mailing list
firedrake@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake