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Queue: PublicMetaMap
Subject: Problem with Metamap installation
Status: resolved
Created: Tue Mar 19 10:50:57 2013
Resolved: Tue Mar 19 10:51:41 2013
LastUpdated: Tue Mar 19 10:51:41 2013

Subject: Problem with Metamap installation
Creator: 28
Created: 2013-03-19 14:50:57
Transaction: 1863
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Subject: 
Creator: 28
Created: 2013-03-19 14:50:57
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Content: Dear Metamap support,

I am experiencing a problem while installing Metamap on my PC running Ubuntu (12.4). I unzip and finished the installation process, and was able to launch the server successfully. But when running ./bin/metamap12, I got the following error:

... public_mm/bin/metamap12.BINARY.Linux: No such file or directory

The file "metamap12.BINARY.Linux" however does exist under the ./bin directory.

-------------------------------------------------------------
The following are detailed of what I did:

Downloaded public_mm_linux_main_2012.tar.bz2 (md5sum checked) and mv it to
/home/mars/my_install_temp/metamap

$ cd /home/mars/my_install_temp/metamap

$ bunzip2 -c public_mm_linux_main_2012.tar.bz2 | tar xvf -
...

$ cd public_mm

(edited .bashrc to setup JAVA_HOME to "/usr" and include "/home/mars/my_install_temp/metamap/public_mm" in PATH)

$ ./bin/install.sh
...

$
./bin/skrmedpostctl start
Starting skrmedpostctl:
started.

$ ./bin/wsdserverctl start
$Starting wsdserverctl:
started.
[email redacted]:~/my_install_temp/metamap/public_mm$ loading properties file /home/mars/my_install_temp/metamap/public_mm/WSD_Server/config/disambServer.cfg
WSD Server initializing disambiguation methods.
WSD Server databases and disambiguation methods have been initialized.

... (demo hangs)


(In a separate console)

$ ./bin/metamap12
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12 /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux -L 2012 -Z 2012AA
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12: line 113: /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux: No such file or directory

Similarly,

$ echo "lung cancer" | ./bin/metamap12 -I
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12 /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux -L 2012 -Z 2012AA -I
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12: line 113: /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux: No such file or directory


Please help!

Thanks,
Gene

Subject: Problem with Metamap installation - gene hugs <[email redacted]>
          - 2012-12-29 1025.eml

Creator: 28
Created: 2013-03-19 14:50:57
Transaction: 1863
Parent: 140
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Filename: Problem with Metamap installation - gene hugs <[email redacted]> - 2012-12-29 1025.eml
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         Subject: Problem with Metamap installation
         From: gene hugs <[email redacted]>
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         --f46d041826aa7b5b4604d1ff64dd
         Content-Type: text/plain; charset="ISO-8859-1"
         
         Dear Metamap support,
         
         I am experiencing a problem while installing Metamap on my PC running
         Ubuntu (12.4). I unzip and finished the installation process, and was able
         to launch the server successfully. But when running ./bin/metamap12, I got
         the following error:
         
         ... public_mm/bin/metamap12.BINARY.Linux: No such file or directory
         
         The file "metamap12.BINARY.Linux" however does exist under the ./bin
         directory.
         
         -------------------------------------------------------------
         The following are detailed of what I did:
         
         Downloaded public_mm_linux_main_2012.tar.bz2 (md5sum checked) and mv it to
         /home/mars/my_install_temp/metamap
         
         $ cd /home/mars/my_install_temp/metamap
         
         *$ bunzip2 -c *public_mm_linux_main_2012.tar.bz2* | tar xvf -
         ...
         
         $ cd public_mm
         
         (edited .bashrc to setup JAVA_HOME to "/usr" and include
         "/home/mars/my_install_temp/metamap/public_mm" in PATH)
         
         $ ./bin/install.sh
         ...
         
         $** ./bin/skrmedpostctl start
         Starting skrmedpostctl:
         started.
         *
         $ ./bin/wsdserverctl start
         $Starting wsdserverctl:
         started.
         [email redacted]:~/my_install_temp/metamap/public_mm$ loading properties file
         /home/mars/my_install_temp/metamap/public_mm/WSD_Server/config/disambServer.cfg
         WSD Server initializing disambiguation methods.
         WSD Server databases and disambiguation methods have been initialized.
         
         ... (demo hangs)
         
         
         (In a separate console)
         
         $ ./bin/metamap12
         /home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12
         /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux -L
         2012 -Z 2012AA
         /home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12: line 113:
         /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux: No
         such file or directory
         
         Similarly,
         
         $ echo "lung cancer" | ./bin/metamap12 -I
         /home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12
         /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux -L
         2012 -Z 2012AA -I
         /home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12: line 113:
         /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux: No
         such file or directory
         
         
         Please help!
         
         Thanks,
         Gene
         
         *
         *
         
         --f46d041826aa7b5b4604d1ff64dd
         Content-Type: text/html; charset="ISO-8859-1"
         Content-Transfer-Encoding: quoted-printable
         
         Dear Metamap support,

I am experiencing a problem while installin= g Metamap on my PC running Ubuntu (12.4). I unzip and finished the installa= tion process, and was able to launch the server successfully. But when runn= ing ./bin/metamap12, I got the following error:

... public_mm/bin/metamap12.BINARY.Linux: No such file or directory
=
The file "metamap12.BINARY.Linux" however does exist under th= e ./bin directory.

-------------------------------------------------= ------------
The following are detailed of what I did:

Downloaded public_mm_linux= _main_2012.tar.bz2 (md5sum checked) and mv it to
/home/mars/my_install_t= emp/metamap

$ cd /home/mars/my_install_temp/metamap

$ bunzip2 -c public_mm_linux_main_2012.tar.bz2 | tar xvf -
...

$ cd public_mm

(edited .bashrc to setup JAVA_HOME to &qu= ot;/usr" and include "/home/mars/my_install_temp/metamap/public_m= m" in PATH)

$ ./bin/install.sh
...

$
./bin/skrmedpostctl start
Start= ing skrmedpostctl:
start= ed.

$ ./bin/wsdserverctl start
$Starting wsdserverctl:
started.<= br>[email redacted]:~/my_install_temp/metamap/public_mm$ loading properties file /= home/mars/my_install_temp/metamap/public_mm/WSD_Server/config/disambServer.= cfg
WSD Server initializing disambiguation methods.
WSD Server databases and= disambiguation methods have been initialized.

... (demo hangs)
<= br>
(In a separate console)

$ ./bin/metamap12
/home/mars/my_i= nstall_temp/metamap/public_mm/bin/SKRrun.12 /home/mars/my_install_temp/meta= map/public_mm/bin/metamap12.BINARY.Linux -L 2012 -Z 2012AA
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12: line 113: /home= /mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux: No such= file or directory

Similarly,

$ echo "lung cancer"= | ./bin/metamap12 -I
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12 /home/mars/my_in= stall_temp/metamap/public_mm/bin/metamap12.BINARY.Linux -L 2012 -Z 2012AA -= I
/home/mars/my_install_temp/metamap/public_mm/bin/SKRrun.12: line 113: = /home/mars/my_install_temp/metamap/public_mm/bin/metamap12.BINARY.Linux: No= such file or directory


Please help!

Thanks,
Gene


--f46d041826aa7b5b4604d1ff64dd--

Subject: 
Creator: 28
Created: 2013-03-19 14:51:41
Transaction: 1866
Parent: 0
MessageId: [email redacted]
Filename: 
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Content: I was wondering are you running a 64-bit system?   I tested the main  Linux Public MetaMap Distribution (public_mm_linux_main_2012.tar.bz2) on  a Mint Linux 64 bit system (a Ubuntu derivative) and the file  "public_mm/bin/metamap12.BINARY.Linux" was present. 

The error you're see can occur if you are running MetaMap on a 64-bit system which does not have the 32-bit compatibility libraries present.

 The executable file metamap12.BINARY.Linux is a 32-bit binary but one should be able to run it on a 64-bit system provided that you have a 32-bit version of libc-*.so in /lib (as well as a /lib64/libc-*.so). (The locations of these files may vary.) There may also be other 32-bit supporting files that may need to be installed also.

If you're running an Ubuntu or Debian system be sure that the package ia32-libs is installed. You can install it using the command (you must be root to do this):

$ sudo apt-get install ia32-libs

The APT program will install any necessary dependencies as well.

Sincerely,
Willie Rogers
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