User getting `ERROR: Unrecognized Identifier: 'dagmc'` #66

jbae11 · 2020-10-22T22:35:35Z

Hello, I was trying to use the plugin on my Ubuntu 20.04, with Cubit 15.6.

I used the
I'm not sure if I'm doing something wrong, but I wasn't able to open the tar file from the curl command, so I downloaded the one named svalinn-plugin-16.5-u18.04.tgz and followed the instructions from the svalinn-plugin-linux-install.txt. The install script was run on cubit/bin/ and I didn't get any error messages. However when I ran export dagmc on cubit, it said it didn't recognize the dagmc identifier. I'm probably missing something trivial but I can't seem to figure it out. I'm sure this isn't the best place to post this but I didn't find a user group. Can someone help me identify the potential issue please?

Thank you,

The text was updated successfully, but these errors were encountered:

bam241 · 2020-10-23T18:56:09Z

Hi @jbae11
could you link svalinn-plugin-linux-install.txt, I don't know where this is located.

otherwise to install, I would do is:

cd /opt/cubit
sudo tar -xzvf /path/to/Trelis-SDK-16.5.0-u18.04.tar.gz

I am also wondering:

what is the absolute path to you cubit install folder. I seems to me that we hard code some path in the library that corresponds to Trelis not Cubit. @ljacobson64 do you think it might be a problem ?
can you go in cubit/bin, give us the return of pwd, ls plugin/svalinnandreadelf -d libsvalinn_plugin.so` (this should tell us of the problem is the hardcoded path as I suspect...

jbae11 · 2020-10-23T19:34:54Z

Hi @bam241 thank you for the quick reply! I hope you're doing well.

Hi @jbae11
could you link svalinn-plugin-linux-install.txt, I don't know where this is located.

I got it from https://uwmadison.app.box.com/v/dagmc-trelis/file/208482372859

otherwise to install, I would do is:
cd /opt/cubit
sudo tar -xzvf /path/to/Trelis-SDK-16.5.0-u18.04.tar.gz

Where could I get this tar file?

I am also wondering:

* what is the absolute path to you cubit install folder. I seems to me that we hard code some path in the library that corresponds to Trelis not Cubit. @ljacobson64 do you think it might be a problem ?

* can you go in `cubit/bin`,  give us the return of `pwd, `ls plugin/_svalinn_`and`readelf -d libsvalinn_plugin.so` (this should tell us of the problem is the hardcoded path as I suspect...

I get /home/4ib/codes/cubit-15.6/bin for the pwd, and:

(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins/svalinn$ readelf -d libsvalinn_plugin.so 

Dynamic section at offset 0x3dcf0 contains 34 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libcubiti19.so]
 0x0000000000000001 (NEEDED)             Shared library: [libcubit_geom.so]
 0x0000000000000001 (NEEDED)             Shared library: [libmakeWatertight.so]
 0x0000000000000001 (NEEDED)             Shared library: [libMOAB.so.5]
 0x0000000000000001 (NEEDED)             Shared library: [libmcnp2cad.so]
 0x0000000000000001 (NEEDED)             Shared library: [libcubit_util.so]
 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x000000000000001d (RUNPATH)            Library runpath: [/opt/Trelis-16.5/bin:/root/opt/dagmc/lib:/usr/lib/x86_64-linux-gnu/hdf5/serial:/root/opt/svalinn-plugin/DAGMC-Trelis/bld/mcnp2cad]
 0x000000000000000c (INIT)               0x1cc38
 0x000000000000000d (FINI)               0x330f4
 0x0000000000000019 (INIT_ARRAY)         0x23d688
 0x000000000000001b (INIT_ARRAYSZ)       32 (bytes)
 0x000000000000001a (FINI_ARRAY)         0x23d6a8
 0x000000000000001c (FINI_ARRAYSZ)       8 (bytes)
 0x000000006ffffef5 (GNU_HASH)           0x1f0
 0x0000000000000005 (STRTAB)             0x8320
 0x0000000000000006 (SYMTAB)             0x1d38
 0x000000000000000a (STRSZ)              56322 (bytes)
 0x000000000000000b (SYMENT)             24 (bytes)
 0x0000000000000003 (PLTGOT)             0x23e000
 0x0000000000000002 (PLTRELSZ)           20232 (bytes)
 0x0000000000000014 (PLTREL)             RELA
 0x0000000000000017 (JMPREL)             0x17d30
 0x0000000000000007 (RELA)               0x16860
 0x0000000000000008 (RELASZ)             5328 (bytes)
 0x0000000000000009 (RELAENT)            24 (bytes)
 0x000000006ffffffe (VERNEED)            0x167a0
 0x000000006fffffff (VERNEEDNUM)         4
 0x000000006ffffff0 (VERSYM)             0x15f22
 0x000000006ffffff9 (RELACOUNT)          26
 0x0000000000000000 (NULL)               0x0
(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plug

ljacobson64 · 2020-10-23T20:53:47Z

The tarball you downloaded was only tested with Trelis 16.5. It may or may not work with Cubit 15.6. In any case, your output of readelf -d libsvalinn_plugin.so shows that it is looking for Trelis in /opt/Trelis-16.5, not in /opt/cubit-15.6. If you create a symlink so that /opt/Trelis-16.5 points to /opt/cubit-15.6, then the plugin may work if it turns out it's compatible with Cubit 15.6.

jbae11 · 2020-10-25T19:39:13Z

@ljacobson64 thank you for the answer, terribly sorry but how can I do that? my cubit path is /home/4ib/codes/cubit-15.6

jbae11 · 2020-10-28T20:35:30Z

@bam241 helped me out via a call and we made a new plugin build that works now for Cubit-15.6. It recognized and got the dagmc plugin. However, when I ran the export command, cubit crashed with message:

(base) 4ib@LAP123233:~/codes/cubit-15.6$ ./cubit 
/home/4ib/codes/cubit-15.6/bin/clarox: symbol lookup error: /home/4ib/codes/cubit-15.6/bin/plugins/libdagmc_export_plugin.so: undefined symbol: _ZN11CubitStringC1ERKS_

any ideas what this might mean?
thanks

bam241 · 2020-10-28T20:37:48Z

can you give us a readelf -d on libdagmc_export_plugin.so ?

bam241 · 2020-10-28T20:40:09Z

libdagmc_export_plugin.so should not leave in the plugin you have, maybe it is remaining from previous install you did ?

I would suggest to clean from any the Svalinn plugin lib and reinstall

jbae11 · 2020-10-28T20:42:01Z

(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins$ readelf -d libdagmc_export_plugin.so 

Dynamic section at offset 0x40d08 contains 34 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libcubiti19.so]
 0x0000000000000001 (NEEDED)             Shared library: [libcubit_geom.so]
 0x0000000000000001 (NEEDED)             Shared library: [libmakeWatertight.so]
 0x0000000000000001 (NEEDED)             Shared library: [libMOAB.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libcubit_util.so]
 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x000000000000000e (SONAME)             Library soname: [libdagmc_export_plugin.so]
 0x000000000000000f (RPATH)              Library rpath: [/opt/Trelis-16.0/bin:/home/shriwise/dagmc_blds/dagmc/lib]
 0x000000000000000c (INIT)               0x21160
 0x000000000000000d (FINI)               0x36354
 0x0000000000000019 (INIT_ARRAY)         0x240708
 0x000000000000001b (INIT_ARRAYSZ)       24 (bytes)
 0x000000000000001a (FINI_ARRAY)         0x240720
 0x000000000000001c (FINI_ARRAYSZ)       8 (bytes)
 0x000000006ffffef5 (GNU_HASH)           0x1f0
 0x0000000000000005 (STRTAB)             0x9620
 0x0000000000000006 (SYMTAB)             0x26d8
 0x000000000000000a (STRSZ)              68552 (bytes)
 0x000000000000000b (SYMENT)             24 (bytes)
 0x0000000000000003 (PLTGOT)             0x241000
 0x0000000000000002 (PLTRELSZ)           21048 (bytes)
 0x0000000000000014 (PLTREL)             RELA
 0x0000000000000017 (JMPREL)             0x1bf28
 0x0000000000000007 (RELA)               0x1abf0
 0x0000000000000008 (RELASZ)             4920 (bytes)
 0x0000000000000009 (RELAENT)            24 (bytes)
 0x000000006ffffffe (VERNEED)            0x1ab30
 0x000000006fffffff (VERNEEDNUM)         4
 0x000000006ffffff0 (VERSYM)             0x1a1e8
 0x000000006ffffff9 (RELACOUNT)          23
 0x0000000000000000 (NULL)               0x0

bam241 · 2020-10-28T20:43:16Z

this should not be there.... remove everything related to svalinn and install the plugin again :)

jbae11 · 2020-10-28T20:45:10Z

I did that, and still crashed, but with a different message :)

/home/4ib/codes/cubit-15.6/bin/clarox: symbol lookup error: /home/4ib/codes/cubit-15.6/bin/plugins/libsvalinn_plugin.so: undefined symbol: _ZN4moab12GeomTopoToolC1EPNS_9InterfaceEbmbb

bam241 · 2020-10-28T20:46:31Z

readelf -d libsvalinn_plugin.so ?

jbae11 · 2020-10-28T20:47:24Z

(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins$ readelf -d libsvalinn_plugin.so 

Dynamic section at offset 0x18ca8 contains 35 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libcubiti19.so]
 0x0000000000000001 (NEEDED)             Shared library: [libMOAB.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libmakeWatertight.so]
 0x0000000000000001 (NEEDED)             Shared library: [libmcnp2cad.so]
 0x0000000000000001 (NEEDED)             Shared library: [libiGeom.so]
 0x0000000000000001 (NEEDED)             Shared library: [libcubit_geom.so]
 0x0000000000000001 (NEEDED)             Shared library: [libcubit_util.so]
 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x000000000000001d (RUNPATH)            Library runpath: [/opt/Trelis-16.5/bin:/opt/Trelis-16.5/bin/plugins/svalinn]
 0x000000000000000c (INIT)               0x62b8
 0x000000000000000d (FINI)               0x14f7c
 0x0000000000000019 (INIT_ARRAY)         0x218678
 0x000000000000001b (INIT_ARRAYSZ)       40 (bytes)
 0x000000000000001a (FINI_ARRAY)         0x2186a0
 0x000000000000001c (FINI_ARRAYSZ)       8 (bytes)
 0x000000006ffffef5 (GNU_HASH)           0x1f0
 0x0000000000000005 (STRTAB)             0x1c70
 0x0000000000000006 (SYMTAB)             0x590
 0x000000000000000a (STRSZ)              8334 (bytes)
 0x000000000000000b (SYMENT)             24 (bytes)
 0x0000000000000003 (PLTGOT)             0x219000
 0x0000000000000002 (PLTRELSZ)           3624 (bytes)
 0x0000000000000014 (PLTREL)             RELA
 0x0000000000000017 (JMPREL)             0x5490
 0x0000000000000007 (RELA)               0x3fd8
 0x0000000000000008 (RELASZ)             5304 (bytes)
 0x0000000000000009 (RELAENT)            24 (bytes)
 0x000000006ffffffe (VERNEED)            0x3ee8
 0x000000006fffffff (VERNEEDNUM)         4
 0x000000006ffffff0 (VERSYM)             0x3cfe
 0x000000006ffffff9 (RELACOUNT)          8
 0x0000000000000000 (NULL)               0x0

with this:

(base) 4ib@LAP123233:/opt/Trelis-16.5$ pwd
/opt/Trelis-16.5
(base) 4ib@LAP123233:/opt/Trelis-16.5$ ls -l
total 112
lrwxrwxrwx 1 root root    31 Oct 28 15:26 bin -> /home/4ib/codes/cubit-15.6/bin/

bam241 · 2020-10-28T20:48:42Z

and ldd libsvalinn_plugin.so| grep MOAB ?

jbae11 · 2020-10-28T20:49:38Z

(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins$ ldd libsvalinn_plugin.so | grep MOAB
	libMOAB.so.0 => /opt/Trelis-16.5/bin/plugins/svalinn/libMOAB.so.0 (0x00007fa1dacf2000)

with:

(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins/svalinn$ ls
libdagmc.so                libiGeom.so           libMOAB.so        libpyne_dagmc.so
libhdf5_serial.so.100      libmakeWatertight.so  libMOAB.so.0      libsvalinn_plugin.so
libhdf5_serial.so.100.0.1  libmcnp2cad.so        libMOAB.so.0.0.0  libuwuw.so

bam241 · 2020-10-28T20:50:07Z

ldd libsvalinn_plugin.so| grep iGeom ?

jbae11 · 2020-10-28T20:51:01Z

this might be it:

(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins/svalinn$ cd ..
(base) 4ib@LAP123233:~/codes/cubit-15.6/bin/plugins$ ldd libsvalinn_plugin.so |grep iGeom
	libiGeom.so => /opt/Trelis-16.5/bin/libiGeom.so (0x00007f3d1563e000)

bam241 · 2020-10-28T20:51:54Z

this is weird

bam241 · 2020-10-28T20:52:51Z

you should have something like /opt/Trelis-17.1/bin/plugins/svalinn/libiGeom.so

have you trying to install Moab and put some of the library somewhere in cubit ?

jbae11 · 2020-10-28T20:53:53Z

yeah i copied that file to one down (in plugins) and got a different error:

	/home/4ib/codes/cubit-15.6/bin/clarox: symbol lookup error: /home/4ib/codes/cubit-15.6/bin/plugins/libsvalinn_plugin.so: undefined symbol: _ZN11CubitStringC1ERKS_

I think the paths to the files are a bit off, like they're either on bin or bin/plugin, not bin/plugin/svalinn

bam241 · 2020-10-28T20:56:40Z

I don;'t understand what that means....
but my guess is the libiGeom that is in you bin folder is the one you build yourself, and don't had the right compiling flags.
if you removed it, then Cubit must have fallen back on the one we ship with the plugin, and then you have a problem because your version of cubit is not compatible with the version fo Trelis I used to build the plugin....

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User getting `ERROR: Unrecognized Identifier: 'dagmc'` #66

User getting `ERROR: Unrecognized Identifier: 'dagmc'` #66

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User getting ERROR: Unrecognized Identifier: 'dagmc' #66

User getting ERROR: Unrecognized Identifier: 'dagmc' #66

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User getting `ERROR: Unrecognized Identifier: 'dagmc'` #66

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