[firedrake] New Firedrake dependency - libspatialindex

[Justin Chang]

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 at 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 at 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 at 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
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>>>
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>>
>>
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