Ubuntu Scidb 15.7 install error


#1

Hello -

I’m still trying to install Scidb into VMware Fusion (on my MAC) running Ubuntu 14.04. I have made it through the “./run.py setup” and “./run.py make-j4” steps but am failing on the “./run.py install” step (I am loading Community Edition).

I initially had an error indicating Unterminated quoted string. I found a post stating the SCIDB_INSTALL_PATH must be something other than /opt/scidb/$SCIDB_VER, so I changed that and re-ran the setup and make commands. My SCIDB_INSTALL_PATH is now /usr/local/scidbtrunk/stage/install.

When I try to install, now I get the error:

-- Installing: /usr/local/scidbtrunk/stage/install/include/util/Platform.h
-- Installing: /usr/local/scidbtrunk/stage/install/include/util/LockManager.h
[sudo] password for scidb: 
mydb is the result
Deleting mydb...
DROP DATABASE
UPDATE 1
GRANT
Sample of connection string:
host=localhost port=5432 dbname=mydb user=mydb password=mydb
scidb.py: ERROR: (REMOTE) Remote command exceptions:
Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string

run.py: ERROR: Command install failed: Abnormal return code: 1 on command ['/usr/local/scidbtrunk/stage/install/bin/scidb.py', 'initall-force', 'mydb', '/usr/local/scidbtrunk/stage/install/etc/config.ini']
run.py: ERROR: Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests
$

My /usr/local/scidbtrunk/stage/install/etc/config.ini file looks like:

$ more config.ini
[mydb]
server-0=127.0.0.1,3
db_user=mydb
install_root=/usr/local/scidbtrunk/stage/install
pluginsdir=/usr/local/scidbtrunk/stage/install/lib/scidb/plugins
logconf=/usr/local/scidbtrunk/stage/install/share/scidb/log1.properties
base-path=/opt/scidb/15.7/scidbtrunk/stage/DB-mydb
base-port=1239
interface=eth0
redundancy=1
# "trust" - anyone can connect without a password 
#"password" - user supplies a password that goes to coordinator as free 
text - username & password are stored in SciDB.
security=trust
$ pwd
/usr/local/scidbtrunk/stage/install/etc
$ 

Any ideas on what I am doing wrong?

Thanks - Lynn


#2

I’m working on this…


#3

I can not reproduce it.

Here is what I did:

I pulled down the source tgz
gunzip scidb-15.7.0.9267.tgz
tar -xf scidb-15.7.0.9267.tar
cd scidb-15.7.0.9267/

added to the end of .bashrc:

export SCIDB_VER=15.7
export SCIDB_INSTALL_PATH=/usr/local/scidbtrunk/stage/install
export SCIDB_BUILD_TYPE=Debug
export PATH=$SCIDB_INSTALL_PATH/bin:$PATH
export MALLOC_CHECK_=3
export MALLOC_PERTURB_=127

and sourced it (. ~/.bashrc)

./run.py setup
./run.py make -j4

sudo mkdir /usr/local/scidbtrunk
sudo chown scidb:scidb /usr/local/scidbtrunk/

./run.py install

No error. I was able to start SciDB and iquery it.

What did you do differently than I did ?


#4

Where you created /usr/local/scidbtrunk and did the chown, I believe I created /usr/local/scidbtrunk/stage/install and then did a chown/chgrp. Should I have stopped at /usr/local/scidbtrunk?

I’ll try doing this again and only creating down to scidbtrunk.


#5

I am logged in as scidb, sitting in directory /opt/scidb/15.7/scidbtrunk

I deleted the stage/install directories under /usr/local/scidbtrunk.

then I re-ran

./run.py setup
./run.py make -j4

All was good. /usr/local/scidbtrunk is setup with owner/group scidb/scidb,

$ ls -ltr /usr/local/scidbtrunk
total 4
drwxrwxr-x 3 scidb scidb 4096 Oct  9 15:24 stage
$ 

Now run:

./run.py install

I get the same error:

Mapper.h
-- Installing: /usr/local/scidbtrunk/stage/install/include/util/TsvParser.h
-- Installing: /usr/local/scidbtrunk/stage/install/include/util/InjectedError.h
-- Installing: /usr/local/scidbtrunk/stage/install/include/util/CoordinatesToKey.h
-- Installing: /usr/local/scidbtrunk/stage/install/include/util/Platform.h
-- Installing: /usr/local/scidbtrunk/stage/install/include/util/LockManager.h
[sudo] password for scidb: 
mydb is the result
Deleting mydb...
DROP DATABASE
UPDATE 1
GRANT
Sample of connection string:
host=localhost port=5432 dbname=mydb user=mydb password=mydb
scidb.py: ERROR: (REMOTE) Remote command exceptions:
Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string

run.py: ERROR: Command install failed: Abnormal return code: 1 on command ['/usr/local/scidbtrunk/stage/install/bin/scidb.py', 'initall-force', 'mydb', '/usr/local/scidbtrunk/stage/install/etc/config.ini']
run.py: ERROR: Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests
scidb@lynn-virtual-machine:/opt/scidb/15.7/scidbtrunk$ 

What else can I try? Are there other logs besides the command line output?

Thanks - Lynn


#6

Even I havethe same error


#7

Sorry this will take a while.

Let’s reproduce the problem at the command level.

Run the following and confirm it has same error:

/usr/local/scidbtrunk/stage/install/bin/scidb.p initall-force mydb /usr/local/scidbtrunk/stage/install/etc/config.ini

also make sure the config file listed is what you expect.


#8

Yes - I get the same error:

[code]
lynn@lynn-virtual-machine:~$ su - scidb
Password:
$
$ /usr/local/scidbtrunk/stage/install/bin/scidb.py initall-force mydb /usr/local/scidbtrunk/stage/install/etc/config.ini
scidb.py: ERROR: (REMOTE) Remote command exceptions:
Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string

$[/code]


#9

Thanks.

Next try “-v” switch with the command.
Capture all the output and put it in this discussion.

/usr/local/scidbtrunk/stage/install/bin/scidb.py -v initall-force mydb /usr/local/scidbtrunk/stage/install/etc/config.ini

I’m looking to see where in initAll() it is failing. check_scidb_running, checkMaxPostgresConns, checkRedundancy, init().
Then we can see what is being passed to ssh.


#10

Sorry for the late response - I’ve been out of town. Thanks for your help. Here is the command with the -v option added:

$ /usr/local/scidbtrunk/stage/install/bin/scidb.py -v initall-force mydb /usr/local/scidbtrunk/stage/install/etc/config.ini 
scidb.py: DEBUG: Debug logging is on!
scidb.py: DEBUG: #### Context created by user scidb
scidb.py: DEBUG: ### get_db_password: 127.0.0.1/None/mydb/mydb
scidb.py: DEBUG: Remote command=exec /bin/bash -c $'source ~/.bashrc; ps --no-headers -e -o pid,cmd | awk \'{print $1 " " $2}\' | grep "/opt/scidb/15.7/scidbtrunk/stage/DB-mydb/000/*" | awk \'{print "scidb_J1jUtpIgih"$1}\''
scidb.py: DEBUG: exit codes ([-1])
scidb.py: DEBUG: done ([False])
scidb.py: DEBUG: stderr drained ([False])
scidb.py: DEBUG: stdout drained ([False])
scidb.py: DEBUG: # active (1)
scidb.py: DEBUG: exit codes ([-1])
scidb.py: DEBUG: done ([False])
scidb.py: DEBUG: stderr drained ([False])
scidb.py: DEBUG: stdout drained ([False])
scidb.py: DEBUG: # active (1)
scidb.py: DEBUG: exit codes ([2])
scidb.py: DEBUG: done ([True])
scidb.py: DEBUG: stderr drained ([False])
scidb.py: DEBUG: stdout drained ([True])
scidb.py: DEBUG: # active (1)
scidb.py: DEBUG: exit codes ([2])
scidb.py: DEBUG: done ([True])
scidb.py: DEBUG: stderr drained ([True])
scidb.py: DEBUG: stdout drained ([True])
scidb.py: DEBUG: # active (0)
Traceback (most recent call last):
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 538, in parallelRemoteExec
    raise RuntimeError("Abnormal return code: %s stderr: %s" % (exits[index],errors[index]))
RuntimeError: Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string
scidb.py: DEBUG: Remote command exceptions:
['exec /bin/bash -c $\'source ~/.bashrc; ps --no-headers -e -o pid,cmd | awk \\\'{print $1 " " $2}\\\' | grep "/opt/scidb/15.7/scidbtrunk/stage/DB-mydb/000/*" | awk \\\'{print "scidb_J1jUtpIgih"$1}\\\'\'']
Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string

scidb.py: ERROR: (REMOTE) Remote command exceptions:
Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string

Traceback (most recent call last):
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 2280, in main
    func(parser, args, modArgs, argv)
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 2233, in handle
    args.func()
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 1936, in init_all_force
    initAll(force=True)
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 967, in initAll
    if (check_scidb_running() > 0):
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 1147, in check_scidb_running
    (ret,out,err) = parallelRemoteExec(sshConns,cmds)
  File "/usr/local/scidbtrunk/stage/install/bin/scidb.py", line 545, in parallelRemoteExec
    raise RemoteAppError('Remote command exceptions:\n%s' % e1)
RemoteAppError: Remote command exceptions:
Abnormal return code: 2 stderr: sh: 1: Syntax error: Unterminated quoted string

$ 

#11

I’m thinking there is a disconnect between where its built and where its installed. And the * in the grep is not getting resolved to the string is messed up.

Where is the DB-mydb directory ?

install_root=/usr/local/scidbtrunk/stage/install
base-path=/opt/scidb/15.7/scidbtrunk/stage/DB-mydb


#12

hello, i m a begginner in scidb and i want to install scidb 15.7 . i have read the instructions for in installation in pdf but i failed to install install. anyone can tell step by step how can i install it in ubuntu 14.04?


#13

I am having a similar error installing 15.7 on CentOS 6.3.


#14

Hi @lynnjo

I ran into this problem today. Found a fix. See if this helps you.

Check what you get when you run: ssh scidb@localhost

Here is what I got:

scidb@ksen-VirtualBox:~/scidb_data$ ssh scidb@localhost
Welcome to Ubuntu 14.04.3 LTS (GNU/Linux 3.19.0-39-generic x86_64)

 * Documentation:  https://help.ubuntu.com/

*** System restart required ***
Last login: Fri Dec 18 14:14:17 2015 from localhost
$ 

This shows that the default shell was getting changed after running ssh, and this was causing the error in scidb.py initall …

This probably happened because you did not specify the default shell when you created the scidb user. You can fix this by going to /etc/passwords.

scidb@ksen-VirtualBox:~/scidb_data$ sudo vi /etc/passwd

If the line corresponding to scidb user looks like below:

scidb:x:1001:1001::/home/scidb:

Change it to:

scidb:x:1001:1001::/home/scidb:/bin/bash

Doing this fixed the error on my end.


#15

I was going through SciDB build instruction. I found for Ubuntu 14.04, following steps need to be done if root does not have any password -

  1. set the root password by

sudo passwd root

  1. vi /etc/ssh/sshd_config and on line 28 change

PermitRootLogin without-password

to

PermitRootLogin yes