Comments (12)
Ahh, good find! I think I have a very portable way of fixing this and will implement as soon as possible and let you know for testing.
Thanks!
from singularity.
I updated the ldd dependency resolver to use the default library paths and use LD_LIBRARY_PATH to update the search path. Will you recreate your SAPPs and let me know what you find?
Thank you!
from singularity.
Looks good!
from singularity.
I closed to early. When an application itself requires LD_LIBRARY_PATH set, the libraries are fetched into the sapp, but they are not found on execution. Am I missing something?
from singularity.
Ahhh, that is a good catch. Some variables should be caught and replicated into the SAPP. I'll think about how to do it and implement something when I get to the computer. Let me know if you think of a fix too!
Thanks!!
Sent from my iPhone
On Nov 27, 2015, at 10:33 AM, weidendo [email protected] wrote:
I closed to early. When an application itself requires LD_LIBRARY_PATH set, the libraries are fetched into the sapp, but they are not found on execution. Am I missing something?
—
Reply to this email directly or view it on GitHub.
from singularity.
I just committed a method which will find all libraries in the SAPP and include them in the LD_LIBRARY_PATH. Can you check to see if that is working now? Thanks!
from singularity.
Hmm, no.
I compiled something with ICC, which needs
/opt/intel/composer_xe_2015.5.223/compiler/lib/intel64
to be in LD_LIBRARY_PATH.
...> singularity build heat.spec
Building: heat
Checking paths...
Checking writable...
Evaluating: %packages
Creating template configs
/etc/nsswitch.conf
/etc/resolv.conf
/etc/hosts
Evaluating: hard requirements
Installing file: /bin/sh
Evaluating: %exec
Installing file: /home/weidendo/SW/heat/heat
Evaluating: %files
Invoking dependency check
Installing file: /lib/x86_64-linux-gnu/libm.so.6
Installing file: /opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libiomp5.so
Installing file: /lib/x86_64-linux-gnu/libgcc_s.so.1
Installing file: /lib/x86_64-linux-gnu/libpthread.so.0
Installing file: /lib/x86_64-linux-gnu/libc.so.6
Installing file: /lib/x86_64-linux-gnu/libdl.so.2
Installing file: /lib64/ld-linux-x86-64.so.2
Including SAPPFILE
Calculating container size
Calculating checksums
Writing metadata
Building primary singularity exec driver
Building singularity test runscript
Building singularity main runscript
Running %test...
Cleaning up unpackaged files
Creating output SAPP container
WROTE: heat.sapp
weidendo@lapbode161:~/SW/heat (master)> ./heat.sapp
/home/weidendo/SW/heat/heat: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
What is your way to debug this?
from singularity.
Looking into ~/.sapp-cache/heat/c/singularity:
...
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/lib/x86_64-linux-gnu
/opt/intel/composer_xe_2015.5.223/compiler/lib/intel64"
...
Newline instead of colon?
from singularity.
Woops... Sorry about that! I just committed a fix that will work... Will test as soon as I get into work.
from singularity.
The fix seems to be working for me, but I don't have a use-case on this system with multiple libdirs. Can you confirm the latest commits are working better?
Thanks!
from singularity.
Works fine here.
from singularity.
Excellent, thanks!
from singularity.
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