Installation: Difference between revisions

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=== [[XDS]] package ===

If you are an academic user, as root (on Ubuntu, use "sudo -i" to become root)

If you are an academic user, as root (on Ubuntu, use "sudo -i" as a separate command, to become root):

<pre>

cd /usr/local/bin

wget ~~--no-check-certificate~~ -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -

wget -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -

ln -sf XDS-gfortran_Linux_x86_64/* .

# until 2025-05-02 the XDS tarfile for Linux had a different name:

Line 15:

# ln -sf XDS-INTEL64_Linux_x86_64/* .

</pre>

In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds backup site].

In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds/current backup site].

If you don't have root rights, replace /usr/local/bin by $HOME/bin in the first line above, and make sure that $HOME/bin is in your $PATH (google "linux set path" or similar).

If you want to process data from the [[Eiger]] detector: see below for plugins that allow XDS to read the .h5 files. Similarly for gzip-ed CBF files as mostly collected at EMBL Hamburg.

==== System libraries that the XDS package needs ====

The programs of the XDS package depend on commonly installed libraries. The complete list, with paths and versions, can be obtained on the commandline:

[kay@linux ~]$ ldd $(which xds_par)

linux-vdso.so.1 (0x00007f96ab59d000)

libdl.so.2 => /lib64/libdl.so.2 (0x00007f96ab57a000)

libm.so.6 => /lib64/libm.so.6 (0x00007f96ab49f000)

libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f96ab459000)

libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f96ab43f000)

libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f96ab43a000)

libc.so.6 => /lib64/libc.so.6 (0x00007f96ab200000)

/lib64/ld-linux-x86-64.so.2 (0x00007f96ab59f000)

If any of the libraries is not available, the affected program does not run but the operating system tells you which library is missing. Until recently, Linux distributions came with these libraries pre-installed. However, recently it came to my attention that a minimal version of Ubuntu 24 may not provide the libgomp.so library. If you run this distribution, your system administrator should install the libgomp1 package.

=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]] ===

... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then

wget ~~--no-check-certificate~~ -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh

wget -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh

chmod +x get_folder.sh

./get_folder.sh

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An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.

Alternatively, ~~tkdiff~~ may be installed, or other graphical comparison programs, like meld or ~~kdiff3~~. vimdiff is also nice, and probably already installed.

Alternatively, [https://download.kde.org/stable/kdiff3/ kdiff3] may be installed, or other graphical comparison programs, like meld or tkdiff. vimdiff is also nice, and probably already installed.

For [[Eiger]] data processing, a h5dump binary (version 1.10 req'd for HDF5 data from DLS) and <code>H5ToXDS</code> is installed by the <code>get_folder.sh</code> script into /usr/local/bin. If the script is not used, <code>H5ToXDS</code> should be installed as [[Eiger|explained]], and <code>h5dump</code> should be installed by e.g. <code>yum -y install hdf5</code> (Ubuntu: <code>apt install hdf5-tools</code>) - but make sure that h5dump is version 1.10 or higher when processing HDF5 data from DLS.

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sudo mkdir /usr/local/bin

As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time

'''As an alternative that does not require root for installation''', one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time

mkdir $HOME/bin

echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile

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if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi

cd /usr/local/bin

# if the next command produces an error message, use the --insecure option

curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf -

ln -sf XDS-OSX_64/* .

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now enter the password, and then

if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi

cd /usr/local/bin;

cd /usr/local/bin

curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - ;

# if the next command produces an error message, use the --insecure option

ln -sf XDS-Apple_M1/* . ;

curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf -

ln -sf XDS-Apple_M1/* .

exit

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source $HOME/.profile

# Added by CCP4 package manager:

. '/Applications/ccp4-8.0/bin/ccp4.setup-sh'

source '/Applications/ccp4-8.0/bin/ccp4.setup-sh'

# or

. '/Applications/ccp4-9/bin/ccp4.setup-sh'

source '/Applications/ccp4-9/bin/ccp4.setup-sh'

</pre>If the file does not exist, create it - the easiest way is:

<pre>

echo . /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile

echo source /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile

# or

echo . /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile

echo source /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile

# depending on which CCP4 version you have installed

</pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.

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mkdir -p /usr/local/bin/mac_bin

cd /usr/local/bin/mac_bin

# if the next command produces an error message, use the --insecure option

curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh

chmod +x get_folder.sh

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mkdir -p /usr/local/bin/mac_bin

cd /usr/local/bin/mac_bin

# if the next command produces an error message, use the --insecure option

curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh

chmod +x get_folder_silicon.sh

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In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.sh</code>) script

# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so . On Silicon Macs you can either use the Intel binaries for XDSGUI and XDS, or the Silicon binaries - the latter are recommended. You could in principle mix them but then you have to be careful with what you enter in the LIB= line of XDS.INP; and what you enter in Menu/Preferences/Paths/generic library of XDSGUI.

# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so .

# copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)

# copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>

A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15].

For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon.

@@ Line 6: / Line 6: @@
 === [[XDS]] package ===
-If you are an academic user, as root (on Ubuntu, use "sudo -i" to become root)
+If you are an academic user, as root (on Ubuntu, use "sudo -i" as a separate command, to become root):
 <pre>
   cd /usr/local/bin
-  wget --no-check-certificate -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -
+  wget -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -
   ln -sf XDS-gfortran_Linux_x86_64/* .
 # until 2025-05-02 the XDS tarfile for Linux had a different name:
@@ Line 15: / Line 15: @@
 # ln -sf XDS-INTEL64_Linux_x86_64/* .
 </pre>
-In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds backup site].
+In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds/current backup site].
 If you don't have root rights, replace /usr/local/bin by $HOME/bin in the first line above, and make sure that $HOME/bin is in your $PATH (google "linux set path" or similar).
 If you want to process data from the [[Eiger]] detector: see below for plugins that allow XDS to read the .h5 files. Similarly for gzip-ed CBF files as mostly collected at EMBL Hamburg.
+==== System libraries that the XDS package needs ====
+The programs of the XDS package depend on commonly installed libraries. The complete list, with paths and versions, can be obtained on the commandline:
+ [kay@linux ~]$ ldd $(which xds_par)
+ 	linux-vdso.so.1 (0x00007f96ab59d000)
+ 	libdl.so.2 => /lib64/libdl.so.2 (0x00007f96ab57a000)
+ 	libm.so.6 => /lib64/libm.so.6 (0x00007f96ab49f000)
+ 	libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f96ab459000)
+ 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f96ab43f000)
+ 	libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f96ab43a000)
+ 	libc.so.6 => /lib64/libc.so.6 (0x00007f96ab200000)
+ 	/lib64/ld-linux-x86-64.so.2 (0x00007f96ab59f000)
+If any of the libraries is not available, the affected program does not run but the operating system tells you which library is missing. Until recently, Linux distributions came with these libraries pre-installed. However, recently it came to my attention that a minimal version of Ubuntu 24 may not provide the libgomp.so library. If you run this distribution, your system administrator should install the libgomp1 package.
 === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]]  ===
 ... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then
-  wget --no-check-certificate -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
+  wget -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
   chmod +x get_folder.sh
   ./get_folder.sh
@@ Line 62: / Line 75: @@
 An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.
-Alternatively, tkdiff may be installed, or other graphical comparison programs, like meld or kdiff3. vimdiff is also nice, and probably already installed.
+Alternatively, [https://download.kde.org/stable/kdiff3/ kdiff3] may be installed, or other graphical comparison programs, like meld or tkdiff. vimdiff is also nice, and probably already installed.
 For [[Eiger]] data processing, a h5dump binary (version 1.10 req'd for HDF5 data from DLS) and <code>H5ToXDS</code> is installed by the <code>get_folder.sh</code> script into /usr/local/bin. If the script is not used, <code>H5ToXDS</code> should be installed as [[Eiger|explained]], and <code>h5dump</code> should be installed by e.g. <code>yum -y install hdf5</code> (Ubuntu: <code>apt install hdf5-tools</code>) - but make sure that h5dump is version 1.10 or higher when processing HDF5 data from DLS.
@@ Line 75: / Line 88: @@
   sudo mkdir /usr/local/bin
-As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time
+'''As an alternative that does not require root for installation''', one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time
   mkdir $HOME/bin
   echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile
@@ Line 86: / Line 99: @@
   if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi
   cd /usr/local/bin
+ # if the next command produces an error message, use the --insecure option
   curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf -
   ln -sf XDS-OSX_64/* .
@@ Line 112: / Line 126: @@
 now enter the password, and then
   if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi
-  cd /usr/local/bin;
+  cd /usr/local/bin
-  curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - ;
+ # if the next command produces an error message, use the --insecure option
-  ln -sf XDS-Apple_M1/* . ;
+  curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf -
+  ln -sf XDS-Apple_M1/* .
   exit
@@ Line 136: / Line 151: @@
 source $HOME/.profile
 # Added by CCP4 package manager:
-. '/Applications/ccp4-8.0/bin/ccp4.setup-sh'
+source '/Applications/ccp4-8.0/bin/ccp4.setup-sh'
 # or
-. '/Applications/ccp4-9/bin/ccp4.setup-sh'
+source '/Applications/ccp4-9/bin/ccp4.setup-sh'
 </pre>If the file does not exist, create it - the easiest way is:
 <pre>
-echo . /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile
+echo source /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile
 # or
-echo . /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile
+echo source /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile
 # depending on which CCP4 version you have installed
 </pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.
@@ Line 160: / Line 175: @@
   mkdir -p /usr/local/bin/mac_bin
   cd /usr/local/bin/mac_bin
+ # if the next command produces an error message, use the --insecure option
   curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh
   chmod +x get_folder.sh
@@ Line 167: / Line 183: @@
   mkdir -p /usr/local/bin/mac_bin
   cd /usr/local/bin/mac_bin
+ # if the next command produces an error message, use the --insecure option
   curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh
   chmod +x get_folder_silicon.sh
@@ Line 176: / Line 193: @@
 In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.sh</code>) script
-# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so . On Silicon Macs you can either use the Intel binaries for XDSGUI and XDS, or the Silicon binaries - the latter are recommended. You could in principle mix them but then you have to be careful with what you enter in the LIB= line of XDS.INP; and what you enter in Menu/Preferences/Paths/generic library of XDSGUI.
+# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so .
 # copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)
 # copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>
-A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15].
 For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon.