Re: [firedrake] New Firedrake dependency - libspatialindex
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:
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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)
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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)
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Hi Justin,
On 13 Nov 2015, at 06:18, Justin Chang <jychang48@gmail.com> wrote:
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 $LD_LIBRARY_PATH respectively. But I am getting this error:
g++ -pthread -shared build/temp.linux-x86_64-2.7/firedrake/spatialindex.o -lspatialindex -o /turquoise/users/jychang48/firedrake-deps/firedrake/src/firedrake/firedrake/spatialindex.so /usr/bin/ld: cannot find -lspatialindex collect2: error: ld returned 1 exit status error: command 'g++' failed with exit status 1
I did"mpicc -x c -v -E /dev/null" and saw that /users/jychang48/.local/include is there, but when I look at LIBRARY_PATH, /users/jychang48/.local/lib is not there.
How can I fix this?
LD_LIBRARY_PATH only tells the dynamic loader where to look for libraries. Not the linker. I think in your case you should try running with the LDFLAGS environment variable set to: LDFLAGS="-L/users/jychang48/.local/lib -Wl,-rpath,/users/jychang48/.local/lib" That should result in no need for LD_LIBRARY_PATH. The former bit sets the search path for the linker. The latter tells the linker to bake that search path into the executable. Cheers, Lawrence
Yes that did the trick, thank you very much! On Fri, Nov 13, 2015 at 1:08 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
Hi Justin,
On 13 Nov 2015, at 06:18, Justin Chang <jychang48@gmail.com> wrote:
Hello again,
I am having issues with spatialindex on my RHEL HPC machine (-no_package_manager). I installed spatialindex 1.8.5 from source (w/ prefix=$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?
LD_LIBRARY_PATH only tells the dynamic loader where to look for libraries. Not the linker. I think in your case you should try running with the LDFLAGS environment variable set to:
LDFLAGS="-L/users/jychang48/.local/lib -Wl,-rpath,/users/jychang48/.local/lib"
That should result in no need for LD_LIBRARY_PATH. The former bit sets the search path for the linker. The latter tells the linker to bake that search path into the executable.
Cheers,
Lawrence
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participants (3)
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David Ham
-
Justin Chang
-
Lawrence Mitchell