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    cd /kb
    git clone ssh://kbase@git.kbase.us/dev_container
    cd /kb/dev_container
./bootstrap /kb/runtime
source user-env.sh
cd /kb/dev_container/modules
git clone ssh://kbase@git.kbase.us/assembly
git fetch origin
git checkout RC
make deploy

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Progress so far on project Core

[seb@sal biosal]# ./scripts/lines.sh 
  5742 total
   705 ./engine/actor.c
   681 ./engine/node.c
   313 ./engine/worker.c
   308 ./structures/hash_table.c
   200 ./examples/mock/mock.c
   197 ./examples/ring/sender.c

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mpiexec -n 3 ./example_controller -threads-per-node 9 ~/dropbox/*.fastq
is king
actor 1582086009 spawned controller 571222134
actor 1582086009 synchronizes
actor 1249840463 receives BSAL_ACTOR_SYNCHRONIZE
actor 1582086009 receives BSAL_ACTOR_SYNCHRONIZE
actor 1201373482 receives BSAL_ACTOR_SYNCHRONIZE
actor 1582086009 receives BSAL_ACTOR_SYNCHRONIZED, sending BSAL_ACTOR_YIELD
actor 1582086009, starting controller 571222134
actor 1582086009 is king

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mpiexec -n 3 ./example_controller -threads-per-node 9 ~/dropbox/*.fastq
is king
actor 1020038268 spawned controller 855878001
actor 1020038268 synchronizes
actor 1020038268 receives BSAL_ACTOR_SYNCHRONIZE
actor 1770361225 receives BSAL_ACTOR_SYNCHRONIZE
actor 381171080 receives BSAL_ACTOR_SYNCHRONIZE
actor 1020038268 receives BSAL_ACTOR_SYNCHRONIZED, sending BSAL_ACTOR_YIELD
actor 1020038268, starting controller 855878001
actor 1020038268 is king

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DEBUG MEMORY REQUESTED 1107296256 bytes !
DEBUG MEMORY REQUESTED 1107296256 bytes !
DEBUG MEMORY REQUESTED 1107296256 bytes !
DEBUG MEMORY REQUESTED 1107296256 bytes !
MEMORY 1 s node/0 4668375040 bytes
MEMORY 1 s node/2 4602212352 bytes
MEMORY 1 s node/1 4601540608 bytes
MEMORY 1 s node/3 4602830848 bytes
MEMORY 2 s node/0 4668375040 bytes
MEMORY 2 s node/2 4602212352 bytes

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$ cloc mothur
     814 text files.
     814 unique files.                                          
      46 files ignored.

http://cloc.sourceforge.net v 1.60  T=5.60 s (143.7 files/s, 41055.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                             380          34767          21318         137141

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[boisvert@cetuslac1 biosal]$ git diff
diff --git a/core/system/memory.c b/core/system/memory.c
index 534dd24..c1282f1 100644
--- a/core/system/memory.c
+++ b/core/system/memory.c
@@ -628,12 +628,12 @@ void core_memory_initialize_memory_subsystem()
      */
 #ifdef __bgq__
 
-        /*

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TLB   V EA Range                          RA Range                          Size  ThID WIMGE RWXRWX XSSP TID  TL
----- - ---------------- ---------------- ---------------- ---------------- ----- ---- ----- ------ ---- ---- --
  0:2 V 0004063888000000-0004063888FFFFFF 0000010088000000-0000010088FFFFFF 16MB  1111 -IM-- RWXrw- ---- 0080 00
  0:3 V 0000000000001000-00000000000FFFFF 0000000000001000-00000000000FFFFF 1MB   1111 --M-- R-X--- X--- 0000 00
  1:2 V 0004063889000000-0004063889FFFFFF 0000010089000000-0000010089FFFFFF 16MB  1111 -IM-- RWXrw- ---- 0080 00
  1:3 V 0000000000100000-00000000001FFFFF 0000000000100000-00000000001FFFFF 1MB   1111 --M-- RWX--- ---- 0000 00
  2:1 V 000406388A000000-000406388AFFFFFF 000001008A000000-000001008AFFFFFF 16MB  1111 -IM-- RWXrw- ---- 0080 00
  2:2 V 0000010002000000-0000010002FFFFFF 0000010002000000-0000010002FFFFFF 16MB  1111 -IM-- RW---- ---- 0000 00
  2:3 V 0000000000200000-00000000002FFFFF 0000000000200000-00000000002FFFFF 1MB   1111 --M-- RWX--- ---- 0000 00
  3:2 V

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------------------------------------------------------------------------
Program   : /gpfs/mira-fs1/projects/CompBIO/Projects/automated-tests/spate-Iowa_Native_Prairie_Soil-2014-12-10-20-26-41.spate
------------------------------------------------------------------------
+++ID Rank: 34, TGID: 1, Core: 13, HWTID:3 TID: 355 State: RUN 

0000000001548678
abort
/bgsys/drivers/V1R2M2/ppc64/toolchain/gnu/glibc-2.12.2/stdlib/abort.c:77

0000000001542788

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#include <string>

namespace A
{

class B
{
    public:
        B();
        ~B();