6 Final System Setup

We are at step to put everything together.

  1. Ask Greg for his modified version of openonload driver and install it. Like before, as root, do the following.

    
# mkdir greg 
    # cd greg 
    # tar xvf modified_oo.tar
    # cd openonload-201310-u2/scripts 
    # ./onload_install 
        
    

    In the case the onload driver has been already installed, one might have to uninstall it first.

    
# onload_uninstall
    # ./onload_install 
        
    
  2. On Capture CentOS Linux computer, create a user with username as capture. The UID and GID both equal to 29998. And also make sure the user capture can do "sudo" so it should belong to sudoers.

  3. login to Capture CentOS Linux computer as capture. Ask Greg for his capture program and all the header files. Place this file capture.tar.bz2 in capture's home directory.

    
% tar xjvf capture.tar.bz2
    % cd CAPTURE
    % ls -l
    total 12
    drwxr-xr-x. 2 capture capture 4096 Feb 25 07:15 lib
    drwxr-xr-x. 2 capture capture 4096 Feb 25 13:03 scripts
    drwxr-xr-x. 2 capture capture 4096 Feb 25 07:16 src
    % cd lib
    % make clean && make
    % cd ../src
    % make clean && make 
          
    

    If things go correctly, you will have a compiled program capture in src directory. You might have to install packages expat and expat-devel.

  4. Now it is the moment. Make a directory from SSD_RAID and from it run:

    
% sudo ifconfig eth4 mtu 9000
    % sudo ifconfig eth5 mtu 9000
    % ~capture/CAPTURE/src/capture
        
    

    The program will spit out some monitoring info like this:

    
  20_17_34:Idle     :370, 0:796, 72650:: 2100 76 76: Range 10000 0
      
    

    Pay attention to the value in the place of :796, 72650:. On our system it is :330, 73444:. If you see the two numbers the other way around, swap the two fibrils to SolarFlare card plug position. We have the following spit out lines from our system.

    
    OUTPUT USERID (-u) 29998 
        OUTPUT grouid (-g) 29998 
        Minimum movie size to be saved  (-m) 1.000000 GB
        NOTE: Saving only movies with more than 16 frames 
        NY = 4096 row_start 0 row_end 4096 nx 4096 g_lda 4096  
        Reading Defect file /mnt/falcon/SensorDefects.xml 
        XML start defects 
        XML start row 
        XML start col 
        XML start col 
        XML start point 
        NUMBER of DEFECTS 4 
        TEST g_lda 4096 ny 4096 nx 4096 
        0 : ROW defect 446 : 0 
        1 : Column defect 1199 
        2 : Column defect 1815 
        3 : POINT defect 2987 347 2
        RETURNING 4 
        Read defect file: /mnt/falcon/SensorDefects.xml  with 4 defects
        Correcting for 4 defects 
        CLOSED FILE 
        Gain 609580.732702 (27330.847552) defined using 13649329 points 
        NEW MEAN (excluding defects) 1.000320 dmin 42.203042 dmax 0.818717 IC 16764929
        Gain file read and gain correction stored as gain_2014_02_27-11_48_40.mrc
        Trying to initialize memory for 160 frames 
        Initializing enough memory for 160 frames
        ATTEMPTING to allocate 5121 huge pages for buffer of size  10741612544 bytes 10 GB
        FRAME SIZE 67108864 
        SHMID1 0 
        NOW MEMSET 10741612544 
        AFTER MEMSET 
        Allocate memory for gain and dark reference field 
        MAX number of interfaces 2 
        Alloca interface eth4 
        Alloca interface eth5 
        Global->threads_n 2 
        THREAD id 1 ->vis_n 1 
        THREAD id 0 ->vis_n 1 
        >>>>>>>>>>>>>>>> SET FILTERS 0 
        >>>>>>>>>>>>>>>> SET FILTERS 1 
        Unknown event 
        Unknown event 
        Unknown event 
        Unknown event 
        11_49_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_50_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_51_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_52_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_53_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_54_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_55_41:Idle     :329, 0:329, 73446:: 0 0 0: Range 10000 0 
        11_56_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_57_41:Idle     :329, 0:329, 73446:: 0 0 0: Range 10000 0 
        11_58_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        11_59_41:Idle     :330, 0:329, 73446:: 0 0 0: Range 10000 0 
        12_00_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        12_01_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
        12_02_41:Idle     :330, 0:330, 73446:: 0 0 0: Range 10000 0 
      
    
  5. If you take a single shot Falcon image, you should see MRC files in the directory!