[R-sig-hpc] Rmpi loads 2 versions of the same library

[Dirk Eddelbuettel]

Hi Ei-ji,

On 14 March 2014 at 11:51, Ei-ji Nakama wrote:
| hi,
| 
| 2014-03-14 4:16 GMT+09:00 Ross Boylan <ross at biostat.ucsf.edu>:
| > I also don't know why libmpi.so.0 is preferred to libmpi.so.1 in the
| > explicit load above.
| 
| I also had the sense of incompatibility of this problem.
| Did anyone try in other platforms?(exclude mac and linux)
| The following corrections might be preferable for the time being.

My memory is really foggy as this issue affected me many years ago when I was
both using Open MPI much more and also looking after the Debian packages for
it.  There was an issue with symbols not being found across the various
shared libraries uses by Open MPI.  And now I can't recall if RTLD_GLOBAL
helped, hurt or was required.  These days you know so much more about this
than I do.

On a Debian-based system, I would recommend getting in touch with the current
maintainers. Sylvestre and Manuel know a lot of this.  And of course with
Hao, the Rmpi author. He just responded almost immediately to a recent
(Debian) bug report regarding which file to try dlopen on, and that (I think)
was the same code segment as below.

Lastly, if were in Ross's shoes, I'd simply create a newer, local package
which will avoid the issue of a conflict between which lib to pick...

Dirk

 
| --- Rmpi.orig/src/Rmpi.c    2013-03-27 02:21:49.000000000 +0900
| +++ Rmpi/src/Rmpi.c    2014-03-14 11:36:43.000000000 +0900
| @@ -18,6 +18,7 @@
|  #include "Rmpi.h"
| 
|  #ifdef OPENMPI
| +#define __USE_GNU
|  #include <dlfcn.h>
|  #endif
| 
| @@ -69,13 +70,19 @@
| 
|  #ifndef MAC
|  #ifdef OPENMPI
| -    if (!dlopen("libmpi.so.0", RTLD_GLOBAL | RTLD_LAZY)
| -    && !dlopen("libmpi.so", RTLD_GLOBAL | RTLD_LAZY)){
| -    //&& !dlopen("libmpi.dylib", RTLD_GLOBAL | RTLD_LAZY)
| -     //&& !dlopen("libmpi.1.dylib", RTLD_GLOBAL | RTLD_LAZY)) {
| -       Rprintf("%s\n",dlerror());
| -        return AsInt(0);
| -    }
| +      { /* ifndef from MAC to __linux__ ? if only problem on linux */
| +        Dl_info info_MPI_Init;
| +        int rc = dladdr((void *)MPI_Init, &info_MPI_Init);
| +        if(rc){
| +          if (!dlopen(info_MPI_Init.dli_fname, RTLD_GLOBAL | RTLD_LAZY)){
| +        Rprintf("%s\n",dlerror());
| +        return AsInt(0);
| +          }
| +        }else{
| +          Rprintf("%s\n",dlerror());
| +          return AsInt(0);
| +        }
| +    }
|  #endif
|  #endif
| 
| 
| >
| > Using LD_DEBUG shows
| > 24312:     file=libmpi.so.1 [0];  needed by /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so [0]
| > 24312:     find library=libmpi.so.1 [0]; searching
| > 24312:      search path=/usr/lib64/R/lib:/home/ross/install/lib            (LD_LIBRARY_PATH)
| > 24312:       trying file=/usr/lib64/R/lib/libmpi.so.1
| > 24312:       trying file=/home/ross/install/lib/libmpi.so.1
| >
| > and, later,
| >      24312:     file=libmpi.so.0 [0];  needed by /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so [0]
| >      24312:     find library=libmpi.so.0 [0]; searching
| >      24312:      search path=/usr/lib64/R/lib:/home/ross/install/lib            (LD_LIBRARY_PATH)
| >      24312:       trying file=/usr/lib64/R/lib/libmpi.so.0
| >      24312:       trying file=/home/ross/install/lib/libmpi.so.0
| >      24312:      search cache=/etc/ld.so.cache
| >      24312:       trying file=/usr/lib/libmpi.so.0
| >
| > Does anyone know what's going on?
| >
| > Ross Boylan
| >
| > P.S. This might be relevant:
| >      24300:     calling init: /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so
| >      24300:
| >      24300:     opening file=/home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so [0]; direct_opencount=1
| >      24300:
| >      24300:     /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so: error: symbol lookup error: undefined symbol: R_init_Rmpi (fatal)
| >      24300:     /home/ross/Rlib-3.0.1/Rmpi/libs/Rmpi.so: error: symbol lookup error: undefined symbol: R_init_Rmpi (fatal)
| >
| > _______________________________________________
| > R-sig-hpc mailing list
| > R-sig-hpc at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
| 
| 
| 
| -- 
| Best Regards,
| --
| EI-JI Nakama  <nakama (a) ki.rim.or.jp>
| "\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>
| 
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com