PBS Professional Guide and Cheat Sheet

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  2. PBS Professional user Guide 14.2
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Compiling R-3.4.2 on CentOS 6 with GNU

If you are compiling CentOS 6, you will notice that the R source will not compile without a updated version of zlib, pcre, bzip2. libcurl. There is a very good site on how to compile R on Red Hat Linux

Step 1: Compile R-3.4.2

Download R-3.4.2 from The R Project for Statistical Computing

$ tar -zxvf R-3.4.2.tar.gz
$ ./configure --prefix=/usr/local/RH6_apps/R-3.4.2

During configuring…. error surfaced.

checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are required

Step 2: Compile zlib 1.2.11

a. In your .bashrc

export CFLAGS="-I/usr/local/zlib-1.2.11/include"
export LDFLAGS="-L/usr/local/zlib-1.2.11/lib"

b. Compile zlib-1.2.11

$ wget http://zlib.net/zlib-1.2.11.tar.gz
$ tar -zxvf zlib-1.2.11
$ cd zlib-1.2.11
$ configure --prefix=/usr/local/zlib-1.2.11

Step 3: Compile bzip2
a. Download the bzip2

$ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
$ tar xzvf bzip2-1.0.6.tar.gz
$ cd bzip2-1.0.6

b. Compile bzip2

$ make -f Makefile-libbz2_so
$ make clean
$ make -n install PREFIX=/usr/local/R-3.4.2
$ make install PREFIX=/usr/local/R-3.4.2

Step 4: Compile liblzma or xz

$ wget http://tukaani.org/xz/xz-5.2.3.tar.gz --no-check-certificate
$ tar xzvf xz-5.2.3.tar.gz
$ cd xz-5.2.3
$ ./configure --prefix=/usr/local/xz-5.2.3
$ make -j8
$ make install

Step 5: Compile pcre-8.40

$ wget ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.40.tar.gz
$ tar xzvf pcre-8.40.tar.gz
$ ./configure --prefix=/usr/local/pcre-8.40
$ make -j 8
$ make install

Step 6: Compile libcurl-7.47.1

$ wget  https://curl.haxx.se/download/curl-7.47.1.tar.gz --no-check-certificate
$ tar xzvf curl-7.47.1.tar.gz
$ cd curl-7.47.1
$ ./configure --prefix=/usr/local/curl-7.47.1
$ make -j 8
$ make install

Step 7: Update CFLAGS and LDFLAGS

export CFLAGS="-I/usr/local/zlib-1.2.11/include -I/usr/local/bzip2-1.0.6/include -I/usr/local/xz-5.2.3/include -I/usr/local/pcre-8.40/include -I/usr/local/curl-7.47.1/include/curl"
export LDFLAGS="-L/usr/local/zlib-1.2.11/lib -L/usr/local/bzip2-1.0.6/lib -L/usr/local/xz-5.2.3/lib -L/usr/local/pcre-8.40/lib -L/usr/local/curl-7.47.1/lib"

Step 8: Compile R-3.4.2

$ ./configure --enable-utf8 --prefix=/usr/local/R-3.4.2
$ make -j 8
$ make install

References:

  1. Building R-devel on RedHat Linux 6

Rectifying Corrupted Keytab file on Centrify Client

Do the required Centrify Log Collection. Do take a look at Collecting logs from Centrify Client

If you notice the logs

============

Oct  5 20:19:06 lsf-login2 adclient[16400]: DEBUG <fd:27 PAMVerifyPassword > base.osutil Module=Kerberos : while getting service credentials: Decrypt integrity check failed (reference base/aduser.cpp:1629 rc: -1765328353) Oct  5 20:19:06 lsf-login2 adclient[16400]: DEBUG <fd:27 PAMVerifyPassword > base.aduser Unable to verify user’s credentials: while getting service credentials: Decrypt integrity check failed Oct  5 20:19:06 lsf-login2 adclient[16400]: DIAG  <fd:27 PAMVerifyPassword > daemon.ipcclient validate password caught exception: while getting service credentials: Decrypt integrity check failed Oct  5 20:19:06 lsf-login2 adclient[16400]: WARN  <fd:27 PAMVerifyPassword > audit User ‘user1’ not authenticated: while getting service credentials: Decrypt integrity check failed Oct  5 20:19:06 lsf-login2 adclient[16400]: DEBUG <fd:27 PAMVerifyPassword > daemon.ipcclient2 doPAMVerifyPassword: user ‘jliu024’ not OK: -1765328353 (Kerberos) Oct  5 20:19:06 lsf-login2 adclient[16400]: DEBUG <fd:27 PAMVerifyPassword > daemon.ipcclient2 request ‘PAMVerifyPassword’ complete =======================

To resolve the issue, do the following

# adkeytab -r -u User1

And try to restart adclient again as root

# /usr/share/centrifydc/bin/centrifydc restart

Collecting logs from Centrify Client

On the Centrify Unix server, as root or sudo, please run the following commands:

1. Turn on Centrify debug:

# /usr/share/centrifydc/bin/addebug on
# /usr/share/centrifydc/bin/addebug clear

2. Reproduce the issue, attempt to log-in.

3. Collect adinfo:

# adinfo -t

4. Turn Off Debug

# /usr/share/centrifydc/bin/addebug off

5. Run adquery and dzinfo for the selected Users:

# adquery user -A UserID1 > /tmp/adquery.txt
# dzinfo UserID1 > /tmp/dzinfo.txt

6. Send the Logs to Centrify Support

/var/centrify/tmp/adinfo_support.tar.gz
/tmp/adquery.txt
/tmp/dzinfo.txt