Configure.sh - Files/Directories Not Found

kmosley

I get that now, thanks.

But now this happens:

/sw/eb/sw/binutils/2.40-GCCcore-12.3.0/bin/ld: cannot find -lze_loader: No such file or directory
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:4723: libISSMCore.la] Error 1
make[3]: Leaving directory '/scratch/user/u.km192000/issm-files/trunk/src/c'
make[2]: *** [Makefile:470: all-recursive] Error 1
make[2]: Leaving directory '/scratch/user/u.km192000/issm-files/trunk/src'
make[1]: *** [Makefile:525: all-recursive] Error 1
make[1]: Leaving directory '/scratch/user/u.km192000/issm-files/trunk'
make: *** [Makefile:457: all] Error 2

mathieumorlighem

that one is a bit trickier. The compiler needs to link against libze_loader.so which is probably related to the GPU. You need to find where this library is (sometimes looking at externalpackages/petsc/install/lib/petsc/conf/petscvariables helps, look for where -lze_loader is and there should be a -L<PATH> that tells you the path).

kmosley

I decided to try to do a fresh install as I couldn't find the libraries. Now I am getting the following:

libtool: warning: '/sw/eb/sw/GCCcore/10.3.0/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../lib64/libstdc++.la' seems to be moved
CXXLD issm.exe
./.libs/libISSMCore.so: error: undefined reference to 'dbesj1'
./.libs/libISSMCore.so: error: undefined reference to '__powi4i4'
./.libs/libISSMCore.so: error: undefined reference to 'dbesj0'
./.libs/libISSMCore.so: error: undefined reference to 'for_write_seq_fmt'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:5075: issm.exe] Error 1
make[3]: Leaving directory '/scratch/user/u.km192000/issm-files/trunk/src/c'
make[2]: *** [Makefile:470: all-recursive] Error 1
make[2]: Leaving directory '/scratch/user/u.km192000/issm-files/trunk/src'
make[1]: *** [Makefile:525: all-recursive] Error 1
make[1]: Leaving directory '/scratch/user/u.km192000/issm-files/trunk'
make: *** [Makefile:457: all] Error 2

mathieumorlighem

These are fortran symbols. You need to find which fortran libraries are on your system and add something like this to configure:

   --with-fortran-lib="-L/usr/local/gfortran/lib/ -lgfortran" \

kmosley

An update, I deleted and reinstalled everything. Rather than renaming the directory after downloading it, I left it as 'ISSM' and changed $ISSM_DIR in bashrc accordingly.

I do get this warning when running make, but no errors:

libtool: warning: '/cm/local/apps/gcc/13.1.0/lib/gcc/x86_64-linux-gnu/13.1.0/../../../../lib64/libstdc++.la' seems to be moved

I don't know if this will impact anything But the make and install did work and the program did successfully run an example.

mathieumorlighem

yeah this is just a warning that is out of our hands (libtool sometimes throws out falls positives), just ignore it. Glad to hear reinstalling did the trick!

kmosley

mathieumorlighem Now, when running the Pig region example in matlab, I'm getting:

com.jogamp.opengl.GLException: X11GLXDrawableFactory - Could not initialize shared resources for X11GraphicsDevice[type .x11, connection :1, unitID 0, handle 0x0, owner false, ResourceToolkitLock[obj 0x221ebe23, isOwner false, <42b50776, 6ddb11d9>[count 0, qsz 0, owner <NULL>]]]
at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.createSharedResource(X11GLXDrawableFactory.java:326)
at jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:297)
at java.lang.Thread.run(Thread.java:748)
Caused by: com.jogamp.opengl.GLException: Startup Class Loader-SharedResourceRunner: Unable to create temp OpenGL context(1)
at jogamp.opengl.x11.glx.X11GLXContext.createImpl(X11GLXContext.java:368)
at jogamp.opengl.GLContextImpl.makeCurrentWithinLock(GLContextImpl.java:759)
at jogamp.opengl.GLContextImpl.makeCurrent(GLContextImpl.java:642)
at jogamp.opengl.GLContextImpl.makeCurrent(GLContextImpl.java:580)
at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.createSharedResource(X11GLXDrawableFactory.java:297)
... 2 more

PigRegion
MATLAB has experienced a low-level graphics error, and may not have drawn correctly.
Read about what you can do to prevent this issue at Resolving Low-Level Graphics Issues then restart MATLAB.
To share details of this issue with MathWorks technical support,
please include this file with your service request.
Couldn't create JOGL canvas--using painters
Couldn't create JOGL canvas--using painters
Couldn't create JOGL canvas--using painters
Couldn't create JOGL canvas--using painters
Couldn't create JOGL canvas--using painters

Is this related to this library? I did get the matlab configure error as well:
checking for MATLAB... configure: error: Couldn't find mex.h... check your installation of MATLAB

mathieumorlighem

Ho can you run the Pig tutorial if you could not configure with MATLAB?

mathieumorlighem

and this error looks like an internal warning for MATLAB that you can fix e.g. https://askubuntu.com/questions/867809/matlab-com-jogamp-opengl-glexception-x11glxdrawablefactory-error

kmosley

I am using a cluster based version of MATLAB so I wouldn't need to start it from my end.

Also, for the errors, I start following the instructions and I get the initial image, but no menu options as are present. I also have no option for "exptool"; it sees it as an unrecognized function of variable.

justinquinn

kmosley "cluster based version" So everything is being sent over a window server? What are you using to achieve this? Xterm?

If exptool is not available to MATLAB, I would imagine most of the other functionality would be missing too. How are you starting MATLAB?

kmosley

justinquinn We are using noVNC/TurboVNC. We request an allocation (RAM, cores, time,
etc) to use with MATLAB, then we can launch from this area when the resources are free

mathieumorlighem

I don't recommend installing ISSM with the MATLAB interface on a cluster, but just compile ISSM's executable. The MATLAB interface is only for pre and post processing and should only be used on local servers.

justinquinn

kmosley As Mathieu mentioned, the typical setup when using a cluster is (1) do model setup in MATLAB on a local machine (ISSM installation on local machine includes all MATLAB modules and external packages, but no ISSM executables), (2) solve, which sends solution request to the server using the cluster class you have attached to md, (3) do some stuff with the solution results in MATLAB on your local machine.

If you really want to do what you're describing, you would have to treat the MATLAB instance on the cluster as your "local" machine, and it would require the local installation described above. I don't know how feasible this is, but if you are able to compile and install software to your home directory on this cluster, can point the configuration to the MATLAB installation directory (i.e. somewhere on shared disk space), and if these locations on disk are not ephemeral, you should be able to do it. Note that you would still need the second ISSM installation described, wherein the ISSM executables are available to the compute nodes raised for the job, and you would need to create a custom cluster class (refer to $ISSM_DIR/src/m/classes/clusters and https://issm.ess.uci.edu/trac/issm/) to handle communication.

kmosley

justinquinn Not to go into too far of a tangent, but would performance be limited by the specs of the local machine (RAM, cores, etc) when preparing bin files for large simulations?

justinquinn

kmosley To some extent, yes. I can't really tell you what all the inflection points are for specs that move a machine from "unusable" to "usable", suffice it to say that if the local machine can efficiently startup and run MATLAB, bin read/write time should not be an issue.

kmosley

I decided to use MATLAB on my PC. Also, the "low level graphics error" jogamp error was solved by adding -softwareopengl after a space after matlab.

The libstdc++ error was dealt with by using an LD_Preload. I got an MPI f2C error, which led me to add another path to the preload. This is what I ended up with:

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:"${ISSM_DIR}/externalpackages/petsc/install/lib/libmpi.so:${ISSM_DIR}/externalpackages/petsc/install/lib/libmpifort.so" matlab -softwareopengl

Thanks!