pulling useful information from G03/G09 calculations

A short while after I began grad school, which was years ago now, I realized that checking on the progress of a G03/G09 calculation often required sifting through massive amounts of detritus. Rather than use less and then search through the entire file, I began learning grep, sed, and awk. This post deals with the first command, grep, and how to make custom versions that can pull out specific information. Perhaps the example I use most often is checking on the progress of a geometry optimization. G03/G09 spit out the 4 convergence criteria after each iteration, as shown below.

$ grep -iA3 "maximum force" test.log
 Maximum Force            0.009759     0.000450     NO 
 RMS     Force            0.001640     0.000300     NO 
 Maximum Displacement     0.380695     0.001800     NO 
 RMS     Displacement     0.042164     0.001200     NO 
--
 Maximum Force            0.001122     0.000450     NO 
 RMS     Force            0.000200     0.000300     YES
 Maximum Displacement     0.117795     0.001800     NO 
 RMS     Displacement     0.034630     0.001200     NO 
--
 Maximum Force            0.000796     0.000450     NO 
 RMS     Force            0.000091     0.000300     YES
 Maximum Displacement     0.290041     0.001800     NO 
 RMS     Displacement     0.065495     0.001200     NO 
--
 Maximum Force            0.000462     0.000450     NO 
 RMS     Force            0.000095     0.000300     YES
 Maximum Displacement     0.245764     0.001800     NO 
 RMS     Displacement     0.018789     0.001200     NO 
--
 Maximum Force            0.000530     0.000450     NO 
 RMS     Force            0.000087     0.000300     YES
 Maximum Displacement     0.268022     0.001800     NO 
 RMS     Displacement     0.026751     0.001200     NO 
--
 Maximum Force            0.000268     0.000450     YES
 RMS     Force            0.000051     0.000300     YES
 Maximum Displacement     0.268678     0.001800     NO 
 RMS     Displacement     0.020944     0.001200     NO 

The above command grew tedious when I wanted to monitor more than a couple jobs, hence I made an alias in the .bashrc file in my home directory. This way I only had to type the alias and not the entire grep line.

# extracts geometry convergence criteria
alias grepmax='grep -A3 -i "maximum force"'

# extracts time stamps for each CCSD gradient calc
alias grepccsd='grep "Leave Link  106"'

# extracts the number of steps taken during a geometry opt, IRC, or PES scan
alias grepstep='grep "Step number"'

# extracts the rotational constants (in GHz)
alias greprot='grep "Rotational constants"'

# extracts the harmonic vibrational frequencies (3 columns)
alias grepfreq='grep "Frequencies"'

# extracts the G3 energy (at 0 K and at finite T, but not the enthalpy or free energy)
alias grepg3='grep "G3(0 K)"'

G03 failing with "end of file in zsymb"

I recently came across an error I had not seen before while running Gaussian03. Right after the input file is read was the line,

End of file in ZSymb.

I had deleted one too many blank lines after the geometry input (G03 needs at least one), and adding a new line back in at the end fixed this right up.

radeon 7xxx video cards throttling

I have several rigs with 2 x 7950 or 2 x 7970 and on some of them (m4a79t + 7950 and m5a97 r2.0 + 7950) the gpu and memory clock is throttled under high load. After some searching around I found this utility that enables the cards to increase the power consumption of each card (gcc and the amd adl-sdk are required):

https://bitcointalk.org/index.php?topic=8384.0

I have included the code here for the impatient.

#include <iostream>
#include <cstdlib>
#include <adl_sdk.h>

using namespace std;

extern "C"
{
    int ADL_Main_Control_Create (ADL_MAIN_MALLOC_CALLBACK, int);
    int ADL_Adapter_NumberOfAdapters_Get(int *);
    int ADL_Overdrive5_PowerControl_Set(int, int);
    int ADL_Overdrive5_PowerControl_Get(int, int *, int *);
}

void* __stdcall Alloc ( int iSize )
{
    void* lpBuffer = malloc ( iSize );
    return lpBuffer;
}

void __stdcall ADL_Main_Memory_Free ( void** lpBuffer )
{
    if ( NULL != *lpBuffer )
    {
        free ( *lpBuffer );
        *lpBuffer = NULL;
    }
}

int main()
{
        int adapters, a=99, b=99;
        if(ADL_Main_Control_Create (Alloc, 1) != ADL_OK)
        {
                cout << "ADL initialization error!" << endl;
                return -1;
        }
        
        if(ADL_Adapter_NumberOfAdapters_Get(&adapters) != ADL_OK)
        {
                cout << "Cannot get the number of adapters!" << endl;
                return -1;
        }
        cout << "Found " << adapters << " adapters" << endl;
        for(int i=0; i<adapters; i++)
        {
                if(ADL_Overdrive5_PowerControl_Set(i, 10) != ADL_OK)
                {
                        cout << "Failed to set " << i << " power control" << endl;
                        return -1;
                } else { cout << "Value set for " << i << endl; }
                
                if(ADL_Overdrive5_PowerControl_Get(i, &a, &b) != ADL_OK)
                {
                        cout << "Failed to get " << i << " power control" << endl;
                        return -1;
                }
                cout << "result: " << a << "%, b: " << b << endl;
        }
        return 0;
}

The key line here is if(ADL_Overdrive5_PowerControl_Set(i, 10) != ADL_OK), and you can change the 10 to any integer up to 20. In my case 5 didn't quite work, so I had to use 10. Then to compile it you use g++, and run it using the 2nd line.

# g++ -DLINUX -o powercontrol powercontrol.cpp -latiadlxx

# ./powercontrol

Found 12 adapters

Value set for 0

result: 10%, b: 0

Value set for 1

result: 10%, b: 0

Value set for 2

result: 10%, b: 0

Value set for 3

result: 10%, b: 0

Value set for 4

result: 10%, b: 0

Value set for 5

result: 10%, b: 0

Value set for 6

result: 10%, b: 0

Value set for 7

result: 10%, b: 0

Value set for 8

result: 10%, b: 0

Value set for 9

result: 10%, b: 0

Value set for 10

result: 10%, b: 0

Value set for 11

result: 10%, b: 0

When X/kdm do not start properly

These problems go into the pile labeled, "duh, I should have tried that first." Inevitably when I make changes to the graphics hardware or complete a new install of gentoo I get to the final stage of starting X and am left with a black screen (the monitor is still receiving a signal, there's just nothing there). Usually I check Xorg.0.log and kdm.log and find that there were no issues. In this case it probably means I forgot to set the opengl renderer.

# eselect opengl set ati

After a reboot the system comes right up into kde.

The second variation is an old school X cursor, but nothing else resembling a gui (black screen), and Xorg.0.log whines about fglrx_dri.so. In this case I needed to switch the order of the graphics cards in my xorg.conf. The below command spits out the graphics adapters, and the first column is the information we want to put into xorg.conf. In this case I already had the correct pci-e device numbers, but I had them in the wrong order. A simple swap of 2:0:0 and 6:0:0 in xorg.conf (NOTE the syntax change when putting these into xorg.conf) and everything was back to functional. (SIDE NOTE: removing a graphics adapter can alter these numbers, in this rig with one card it sits at 05:00.0)

# lspci | grep -i vga

02:00.0 VGA compatible controller: Advanced Micro Devices [AMD] nee ATI Tahiti XT [Radeon HD 7970]

06:00.0 VGA compatible controller: Advanced Micro Devices [AMD] nee ATI Tahiti XT [Radeon HD 7970]

xorg.conf lines

Section "Device"

        Identifier  "aticonfig-Device[0]-0"

        Driver      "fglrx"

        BusID       "PCI:6:0:0"

EndSection

Section "Device"

        Identifier  "aticonfig-Device[1]-0"

        Driver      "fglrx"

        BusID       "PCI:2:0:0"

EndSection

To give a bit of background about my Linux usage; I began with Mandrake, Suse, and Redhat back in 2001. By 2004 I decided that if I were ever to become proficient using Linux I needed to use it 24/7. At this point I had been trying Gentoo, so I loaded it on all of my boxes and have bounced around with various spin offs of Gentoo (Vidalinux and Funtoo). These days I have moved back to vanilla Gentoo and generally have a small installation of Ubuntu one each box for installing Gentoo.

I suppose if this blog has a purpose, it is primarily to list problems I've run across and fixed. The hope is that writing these solutions down will help my brain cell remember the solutions the next time around.

Now on to the fun stuff, which was udev automagically renaming ethernet devices. The standard tell comes about during system initialization, and rc screams about not being able to start eth0.

$ ifconfig -a

The above command should show the device labeled as something not eth0 (if you don't see anything promising there at all it could be the kernel does not have the driver you need). Now that we know some sort of network device exists there is hope of fixing it. In this case we need to tell udev to stop being so clever and give us back our preciously boring eth0. The solution I decided upon (there were several, I'll try to find links to the others) was adding a rule to /etc/udev/rules.d.

# ln -s /dev/null /etc/udev/rules.d/80-net-name-slot.rules
# /etc/init.d/udev restart
# /etc/init.d/net.eth0 start