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Old 12-04-2013, 11:51 AM   #1
tonybert
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Default smrt build failure

Greetings, I am trying to build the smrt work-flow (centOS version) on our 16 core unix server running red-hat (v. 5.8). I am continually getting the following errors after running ./bash sort-centos.run (below). I installed glib2.7 and changed my PATH, but i still get these errors:

----- Part 2 of 7: System Prerequisite Check -----

Checking various hardware, OS and software related prerequisites...

LOCALE CHECK: en_US.UTF-8
--> OK: This is an English-language system.
OS CHECK: "Red Hat Enterprise Linux Server release 5.8 (Tikanga)"
--> WARNING: Unsupported Linux distribution.
Checking preqeuisite OS packages...
CPU COUNT: 16
--> OK: You have at 16 CPUs on this server (required: 8).
MEM CHECK: Total Memory is 48161 bytes.
--> OK: You have 3010MB per CPU (required: 1800)

The following warnings were detected in checking system prerequisites:

--> WARNING: Unsupported Linux distribution.

Some of these warnings may not be critical, but may affect performance.
Abort the installation? [Y/n]: n
Detecting DNS names...
/public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/bin/dig: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/lib/libgssapi_krb5.so.2)
/public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/bin/dig: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/lib/libcrypto.so.10)
/public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/bin/dig: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/lib/libxml2.so.2)
/public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/bin/dig: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/lib/libkrb5.so.3)
/public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/bin/dig: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/lib/libkrb5support.so.0)
/public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/usr/bin/dig: /lib64/libc.so.6: version `GLIBC_2.8' not found (required by /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/installerdeps/lib/libselinux.so.1)
installprompter: Error! Encountered unexpected error at 'line 442 /public2/smrtanalysis/install/smrtanalysis-2.1.1.128549/admin/bin/installprompter', bailing out...
smrt_reinstall: Error! Encountered unexpected error at 'line 145 ./smrtanalysis/install/smrtanalysis-2.1.1.128549/admin/bin/smrt_reinstall', bailing out...
smrtanalysis-2.1.1-centos-6.3.run: Error! Encountered unexpected error at 'line 243 smrtanalysis-2.1.1-centos-6.3.run', bailing out...
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Old 12-04-2013, 11:56 AM   #2
GenoMax
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Can you check if a soft link for libc.so.6 exists in /lib64 (to libc-2.x.so)? If it is not there can you create it and try the install again.

Did you get the CentOS v.5.6 package (since that is the closest thing for your OS available on PacBioDevNet)? PacBio installers are mostly OS version sensitive.

Last edited by GenoMax; 12-04-2013 at 12:14 PM.
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Old 12-04-2013, 12:48 PM   #3
tonybert
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greeting genomax, thanks for the help, this is what i tried;

cd /lib64
sudo ln -s libc.so.6 libc-2.x.so

however, i received the same result.
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Old 12-04-2013, 12:52 PM   #4
GenoMax
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Quote:
Originally Posted by tonybert View Post
greeting genomax, thanks for the help, this is what i tried;

cd /lib64
sudo ln -s libc.so.6 libc-2.x.so

however, i received the same result.
You need to replace the "x" with the actual number of the libc-2.x.so file (e.g. libc-2.7.so) you have on your server (should be in the same /lib64 directory).

You may have to remove the first softlink and then recreate it with the right command.
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Old 12-04-2013, 02:00 PM   #5
tonybert
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Hi again, I tried what you suggested, and again, the same result. Just to make sure i'm not messing up the initial installation (and run), i've done the steps required online for PacBio in the installation notes (download smrtanalysis-2.1.1-centos-6.3.run into public2).

SMRT_ROOT=/public2/smrtanalysis
sudo mkdir $SMRT_ROOT
bash smrtanalysis-2.1.1-centos-6.3.run
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Old 12-04-2013, 03:08 PM   #6
GenoMax
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Quote:
Originally Posted by tonybert View Post
Hi again, I tried what you suggested, and again, the same result. Just to make sure i'm not messing up the initial installation (and run), i've done the steps required online for PacBio in the installation notes (download smrtanalysis-2.1.1-centos-6.3.run into public2).

SMRT_ROOT=/public2/smrtanalysis
sudo mkdir $SMRT_ROOT
bash smrtanalysis-2.1.1-centos-6.3.run
I do not want to discourage you but if you are new to unix administration then installing a package like SMRTanalysis is going to be challenging.

As I had indicated earlier PacBio software is sensitive to OS version (that is the reason there are multiple separate installers available on DevNet). Since you are running CentOS 5.8 it would not be advisable to use the 6.3 installer (CentOS 5.x and 6.x have significant differences).

Before we go any further it would be best for you to try the installer for CentOS 5.6 since that is the closest version available that matches your OS. If you own a PacBio machine then their tech support may be able to help you with a remote install (which would be quickest option).
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Old 12-04-2013, 03:13 PM   #7
tonybert
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Hi, you know for some reason I hadn't even noticed your first post, went straight to the soft link... sorry. But yes, i'm not a unix expert, and i'm very discouraged right now... but not by you! Thanks for your help, it is sincerely appreciated.
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Old 12-04-2013, 03:15 PM   #8
GenoMax
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Let us try the installer for 5.6 then. Here is a link to their Wiki that has some useful tips for the installations: https://github.com/PacificBioscience...Analysis-Suite

You may want to uninstall the previous version (for 6.3) by using the instructions on the wiki first.
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Old 12-04-2013, 03:51 PM   #9
tonybert
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Ok, so it got further this time, to 5/7 of the setup. I'm having some trouble providing the correct name/password for the mysql database it seems. When it asked for information pertaining to mysql, i just entered in the defaults on the wiki... thinking i might want to use something different, like my user name?

----- Part 5 of 7: SMRT Portal Database ----

SMRT Portal requires a mysql database in order to keep track of
input SMRT cells, jobs, users, and groups. The database only
manages the web-interface and does not store actual sequence data.
You must have mysql installed and run /etc/init.d/mysqld.

Last edited by tonybert; 12-04-2013 at 06:17 PM.
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Old 12-04-2013, 06:08 PM   #10
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You will need to set MySQL up separately. Representative directions are here: http://www.if-not-true-then-false.co...-red-hat-rhel/ Help with the mysql root password: http://stackoverflow.com/questions/8...-root-password

NOTE: You could set up a configuration that can become a major security threat (specially if your server is accessible from the open internet), not only for your server but others on your local network. I strongly urge you to find someone locally who can help you with this part of the install.

PLEASE redact IP address/server name/user acct information from your previous post ASAP.

Last edited by GenoMax; 12-04-2013 at 06:16 PM.
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