We just recently upgraded to scidb 16.9 community edition. I am unable to connect with python using scidb-py, everything else (shim, iquery, scidbr) appears to be working normally. I have pasted the error below, along with a successful connection using scidbr. We did not notice anything not compiling correctly during the upgrade process, but I suppose it’s possible we missed something.
Any help would be appreciated,
~David.
dwiltsee@hpc083 ~ $ cat /etc/redhat-release
Red Hat Enterprise Linux Server release 6.9 (Santiago)
dwiltsee@hpc083 ~ $ pip freeze | grep scidb
scidb-py==14.10.0
dwiltsee@hpc083 ~ $ ipython
Python 2.7.13 (default, Feb 8 2017, 06:30:30)
Type “copyright”, “credits” or “license” for more information.
IPython 4.2.0 – An enhanced Interactive Python.
? -> Introduction and overview of IPython’s features.
%quickref -> Quick reference.
help -> Python’s own help system.
object? -> Details about ‘object’, use ‘object??’ for extra details.
In [1]: import scidbpy as sci
ValueError Traceback (most recent call last)
in ()
----> 1 sdb = sci.connect(‘http://10.17.17.82:8080’)
/opt/rh/python27/root/usr/lib/python2.7/site-packages/scidbpy/interface.pyc in connect(url, username, password)
1845 password = os.environ.get(‘SCIDB_PASSWORD’, None)
1846
-> 1847 return SciDBShimInterface(url, user=username, password=password)
/opt/rh/python27/root/usr/lib/python2.7/site-packages/scidbpy/interface.pyc in init(self, hostname, user, password, pam, digest)
1635 except Exception as e:
1636 raise ValueError(“Could not connect to a SciDB instance at {0}. {1}”
-> 1637 .format(self.hostname, e))
1638
1639 def login(self, user, password):
ValueError: Could not connect to a SciDB instance at http://10.17.17.82:8080. SystemException in file: src/util/PluginManager.cpp function: findModule line: 101
Error id: scidb::SCIDB_SE_PLUGIN_MGR::SCIDB_LE_CANT_LOAD_MODULE
Error description: Plugin manager error. Cannot load module ‘/opt/scidb/16.9/lib/scidb/plugins/libdense_linear_algebra.so’, dlopen returned ‘/opt/scidb/16.9/lib/scidb/plugins/libdense_linear_algebra.so: undefined symbol: _ZN5scidb11MPIPhysical8setQueryERKSt10shared_ptrINS_5QueryEE’.
#################### End Python / Start R Example ##############################
dwiltsee@hpc083 ~ $ R
R version 3.3.2 (2016-10-31) – "Sincere Pumpkin Patch"
Copyright © 2016 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
’citation()’ on how to cite R or R packages in publications.
Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
’help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.
library(scidb)
Loading required package: bit64
Loading required package: bit
Attaching package bit
package:bit © 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: ‘bit’
The following object is masked from ‘package:base’:
xor
Attaching package bit64
package:bit64 © 2011-2012 Jens Oehlschlaegel (GPL-2 with commercial restrictions)
creators: integer64 seq :
coercion: as.integer64 as.vector as.logical as.integer as.double as.character as.bin
logical operator: ! & | xor != == < <= >= >
arithmetic operator: + - * / %/% %% ^
math: sign abs sqrt log log2 log10
math: floor ceiling trunc round
querying: is.integer64 is.vector [is.atomic} [length] is.na format print
aggregation: any all min max range sum prod
cumulation: diff cummin cummax cumsum cumprod
access: length<- [ [<- [[ [[<-
combine: c rep cbind rbind as.data.frame
for more help type ?bit64
Attaching package: ‘bit64’
The following object is masked from ‘package:bit’:
still.identical
The following objects are masked from ‘package:base’:
:, %in%, is.double, match, order, rank
/ /() _ / _ )
\ / / / // / _ |
//_//// Copyright 2016, Paradigm4, Inc.
sdb = scidbconnect(‘10.17.17.82’)
iquery(sdb, “list(‘macros’)”, return=TRUE)
No name
1 0 func_max
2 1 func_min
3 2 load
4 3 op_avg
5 4 op_count
6 5 op_distinct_count
7 6 op_max
8 7 op_min
9 8 op_now
10 9 op_range
11 10 op_scidbversion
12 11 op_set_cell_attr_1D
13 12 op_set_cell_attr_2D
14 13 op_stdev
15 14 op_sum
16 15 sys_create_array_att
17 16 sys_create_array_aux
18 17 sys_create_array_dim
