06 November 2012

276. Compiling Dalton 2011 on Debian Testing/Wheezy

UPDATE: To deal with basis sets and 'GPOPEN' errors, see bottom of this post
UPDATE2: Because of the basis set issue the code doesn't run in parallel!
UPDATE 3: All issues are solved by -O0 or -O1. The code now works in parallel and you can define basis sets the usual way. Performance-wise? No idea. So you can compile with -O3 or -O2 but the code doesn't read basis sets the intended way, or you use -O1 or -O0 and it works.

THIS WORKS NOW  :)

Original post:
I've been wanting to use dalton for a long time, but it's been difficult to compile dalton 2.0, and I didn't realise until a few days ago that there's a newer version.
See here for a description of how to compile on ROCKS 5.4.3 (i.e. Centos 5.6) which uses gfortran v 4.1. The main difference between compiling on CentOS 5.6 and Debian Wheezy is in how you edit the Makefile.config. More specifically, compile works a whole lot better with -fno-whole-file and -march=native..

Other than that the steps are the same.

In terms of running, there's an issue with the discoverability of the basis sets which I don't really understand. There's a solution to that at the end of the file.

Before you get started you may want to compile ATLAS as shown here: http://verahill.blogspot.com.au/2012/05/compile-atlas-blas-on-debian-testing.html

Alternatively, you should get the ACML libraries.

NOTE: The compile went without a hitch on my AMD II X3, AMD Phenom II X6 and Intel i5-2400.
My AMF FX 8150 is a trickier story though: it failed to compile with acml libs (gfortran64_fma4_int64) for -O3 and -O2, but compiled with -O1 and -O0. The -O1 binary segfaults though. Never tried the -O0 binary.

WARNING: If you run dalton in parallel it will -- for some reason -- delete your scratch folder when the run is over. The scratch directory is defined in the  /opt/dalton/bin/dalton script (TMPDIR)

License:
First go to http://daltonprogram.org/licence/ and fill out the license agreement. Once that's done you'll get an automated email with a license form, which you should print, sign, scan and email to the email address you're given. Once your form has been processed you'll be sent another email with a user name and password. I received my user name and password the next business day.

Go online and download the source file, Dalton2011_release_v0.tgz, and put it in ~/tmp. Sort out where you want your program to end up
sudo mkdir /share/apps/dalton
sudo chown $USER /share/apps/dalton
mkdir /share/apps/dalton/bin /share/apps/dalton/basis /share/apps/dalton/lsdalton

Next,
cd ~/tmp
tar xvf Dalton2011_release_v0.tgz
cd Dalton2011_release/DALTON
./configure 

and answer all the questions:
./configure

------------------------------------------------------------------
   Configuring the DALTON Makefile.config and "dalton" run script
------------------------------------------------------------------

INFO: Operating system from 'uname -s' : Linux
INFO: Processor type   from 'uname -m' : x86_64
No architecture specified, attempting auto-configuration:
This appears to be a -linux architecture. Is this correct? [Y/n] 
--> Installing DALTON on a -linux computer


Note that 64-bit integers are desirable for Cholesky and very large
scale CI, otherwise the most important effect is that some files will be bigger.

If you choose 64-bit integers, be careful that any system library
routines (incl. MPI) also use 64-bit integers!

Do you want 64-bit integers? [y/N] Do you want to install the program in a parallel MPI version? [Y/n] 
-->WARNING: Makefiles for MPI architecture are difficult to guess
   Please compare the generated Makefile.config with local documentation.

   Checking for Fortran compiler ...
   from this list: mpif90 mpiifort ifort pgf95 pgf90 gfortran g95 

Compiler /usr/bin/mpif90 found, use this compiler? [Y/n] 
-->Compiler mpif90 found and accepted.
Is backend compiler gfortran ? [Y/n] 
   Checking for C compiler ...
   from this list: mpicc  mpiicc   icc ecc pgcc gcc 

Compiler /usr/bin/mpicc found, use this compiler? [Y/n] 
-->Compiler mpicc found and accepted.

Testing existence of libraries in this order:
 libacml.a libmkl.so libmkl_p3.a libatlas.a libblas.a
Directory search list for libraries:
  /opt/ATLAS/lib /home/me/tmp/ATLAS/build/lib /lib /usr/local/lib /usr/lib /usr/local/lib/ATLAS /lib64 /usr/lib64 /usr/local/lib64 

Do you want to replace this with your own directory search list? [y/N] Found /opt/ATLAS/lib/libatlas.a, use it? [Y/n] 
-->The following mathematical library(ies) will be used:
   -L/opt/ATLAS/lib -llapack -llapack -lf77blas -latlas


DALTON uses almost 100 Megabytes of static
allocations, in addition to the dynamic allocation.

DALTON has the possibility to reserve an amount of static memory
for storing two-electron integrals in direct and parallel calculations
Storing some or all of the 2-el. integrals in memory will speed up
direct and parallel calculations (and in particular the latter).
NOTE: This will increase the static memory allocation used by DALTON

Would you like to activate the possibility of storing 2-el.int. in memory? [y/N] How many MB to use for storing 2-el. integrals? 
-->Program will be installed with 300 MB (39000000 words) used for storing 2-el. integrals

Maximum amount of work memory for dynamic allocations can be changed
at run time with the environment variable WRKMEM (in REAL*8 words = megabytes/8)
or by using the -M option to the run script: "dalton -M mb ..." (in megabytes).
We recommend at least 200 MB work memory,
larger for correlated calculations, but it should for maximum
efficiency NOT exceed available physical memory per CPU in parallel calculations.

How many MB to use as default for work memory (hit return for default of 1000 MB)? 
-->Program will be installed with a default work memory of 3900 MB (511000000 words)

-->Current directory is /home/me/tmp/Dalton2011_release/DALTON

Use default ../bin as installation directory for DALTON binaries and scripts? [Y/n] Please enter another installation directory: 
-->DALTON executable and script will be placed in /opt/dalton/bin directory


-->Default basis set directory will be /home/me/tmp/Dalton2011_release/DALTON/../basis/

Use this directory as default basis set directory? [Y/n] 
Please choose another default basis set directory (must end with /) 
-->Default basis set directory will be /opt/dalton/basis/


-->Job specific directories under $SCRATCH/$USER
-->will be used for temporary files when running DALTON

Use SCRATCH=/work as default root scratch space in "dalton" run script? [Y/n] Please enter default root scratch directory: 
-->Creating Makefile.config ...
gfortran version 471 prc=x86_64
INFO: Compiling with 32-bit integers.
INFO: Make sure pre-compiled BLAS, MPI etc. libraries are also with 32-bit integers!!!

Proper 64-bit file access detected.

-->Creating the DALTON run-script in /opt/dalton/bin

   The configuration of DALTON has finished succesfully.
   Check compiler flags etc. in Makefile.config and run "make" to get executable.

which generates Makefile.config. Edit it and

  • change the -march to native. 
  • add -fno-whole-file to avoid internal compiler errors
  • change optimisation level to -O1 (O0 is ok, O2 and O3 give GPOPEN problems)

Like this:

ARCH        = linux
#
#
CPPFLAGS      = -DVAR_GFORTRAN -DSYS_LINUX -DVAR_MFDS -D'INSTALL_WRKMEM=131000000' -D'INSTALL_MMWORK=65000000' -D_FILE_OFFSET_BITS=64 -DVAR_MPI -DGFORTRAN=471 -DIMPLICIT_NONE
F90           = mpif90
CC            = mpicc
LOADER        = mpif90
RM            = rm -f
FFLAGS        = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -fbacktrace -fno-whole-file
SAFEFFLAGS    = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -fbacktrace -fno-whole-file
CFLAGS        = -march=native -O1 -ffast-math -funroll-loops -ftree-vectorize -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1
INCLUDES      = -I../include 
MODULES       = -J../modules
LIBS          = -L/opt/ATLAS/lib -llapack -llapack -lf77blas -latlas 
INSTALLDIR    = /opt/dalton/bin
PDPACK_EXTRAS = linpack.o eispack.o gp_zlapack.o gp_dlapack.o
GP_EXTRAS     = 
AR            = ar
ARFLAGS       = rvs
# flags for ftnchek on Dalton /hjaaj
CHEKFLAGS  = -nopure -nopretty -nocommon -nousage -noarray -notruncation -quiet  -noargumants -arguments=number  -usage=var-unitialized
# -usage=var-unitialized:arg-const-modified:arg-alias
# -usage=var-unitialized:var-set-unused:arg-unused:arg-const-modified:arg-alias
#
default : dalton linuxparallel.x
SAFE_FFLAGS_for_ifort = $(FFLAGS)
#
# Parallel initialization
#
MPI_INCLUDE_DIR = 
MPI_LIB_PATH    = -L/usr/lib
MPI_LIB         = -lmpi
#
#
# Suffix rules
# hjaaj Oct 04: .g is a "cheat" suffix, for debugging.
#               'make x.g' will create x.o from x.F or x.c with -g debug flag set.
#
.SUFFIXES : .F .F90 .c .o .i .g .s

.F.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F 

.F.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F > $*.i

.F.g:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(SAFEFFLAGS) -g -c $*.F 

.F.s:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -S -g -c $*.F 

.F90.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F90 

.F90.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F90 > $*.i




make
make install

Now just copy the basis sets and ecp data to the proper location:
cd ../
cp basis/* -R /opt/dalton/basis

and edit your ~/.bashrc;
export PATH=$PATH:/opt/dalton/bin

And you should be good to go.


So far I haven't run all the tests, but
./TEST -dalton /opt/dalton/bin/dalton short

gave
#####################################################################
                              Summary
#####################################################################

ALL TESTS ENDED PROPERLY!

date and time         : Wed Nov  7 11:57:02 EST 2012



GPOPEN errors and how to get around them.

To make the story short: if you use -O3 or -O2 for some reason Dalton can't find the basis sets if you declare them the normal way (-O0 and -O1 take care of the problem). However, using ATOMBASIS it works.

Here's an example. Typically you'd specify the basis set for a whole molecule in your .mol file:

BASIS
STO-3G
DFT PROPERTIES TEST 
This doesn't work with O3
AtomTypes=2 Angstrom
        8.    1     
O -0.141254 0.0998816 0.00000
        1.    2     
H 0.589315 0.718039 0.00000
H -0.922641 0.652406 0.00000

but that leads to errors on the debian (but not centos) builds:
   0: Directories for basis set searches:
     /jobs/dalton:/opt/dalton/basis

 MPI node no.:     0
 Reason: ERROR (GPOPEN) UPON OPENING A FILE


 Node      0:  --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
 ERROR (GPOPEN) UPON OPENING A FILE

and
  Atomic type no.    1
  --------------------
  Nuclear charge:   8.00000
  Number of symmetry independent centers:    1
  Number of basis sets to read;    2
  Basis set file used for this atomic type with Z =   8 :
     "/opt/dalton/basis/                                                                                "


--> ERROR (GPOPEN) UPON TRYING TO OPEN FILE ON UNIT 11
--> with filename /opt/dalton/basis/
--> IOSTAT ERROR CODE RETURNED      21


 QTRACE dump of internal trace stack

 ========================
      level    module
 ========================
          7    GPOPEN      
          6    BASLIB      
          5    READ_MOL    
          4    READIN      
          3    HERMIT      
          2    DALTON      
          1    DALTON main 

whereas

ATOMBASIS
DFT PROPERTIES TEST 
This works with O3
AtomTypes=2 Angstrom
        8.    1    basis=STO-3G 
O -0.141254 0.0998816 0.00000
        1.    2     basis=STO-3G
H 0.589315 0.718039 0.00000
H -0.922641 0.652406 0.00000

works and gives
   0: Directories for basis set searches:
     /opt/dalton/basis:/opt/dalton/basis

 NOTE:    1 informational messages have been issued.
 Check output, result, and error files for "INFO".

and a normal exit:
 CPU time statistics for ABACUS
 ------------------------------

 LINRES     00:00:02      77 %

 TOTAL      00:00:03     100 %


 >>>> Total CPU  time used in ABACUS:   3.21 seconds
 >>>> Total wall time used in ABACUS:   3.22 seconds


                   .-------------------------------------------.
                   | End of Static Property Section (ABACUS) - |
                   `-------------------------------------------'

 >>>> Total CPU  time used in DALTON:   6.04 seconds
 >>>> Total wall time used in DALTON:   6.06 seconds

 
     Date and time (Linux)  : Tue Nov  6 14:54:24 2012
     Host name              : beryllium   

05 November 2012

275. Compiling Dalton 2011 on ROCKS 5.4.3/CentOS

I've previously struggled with Dalton 2.0-cam and given up. I somehow didn't know about Dalton 2011 at that point, but it turns out it's much easier to build. Well, I managed to build it on ROCKS/CentOS (gcc 4.1). I'm still working on the debian version which has a much newer gcc (4.7)

Before you get started you may want to compile ATLAS as shown here: http://verahill.blogspot.com.au/2012/09/rocks-543-atlas-and-gromacs-on-xeon.html

License:
First go to http://daltonprogram.org/licence/ and fill out the license agreement. Once that's done you'll get an automated email with a license form, which you should print, sign, scan and email to the email address you're given. Once your form has been processed you'll be sent another email with a user name and password. I received my user name and password the next business day.

Go online and download the source file, Dalton2011_release_v0.tgz, and put it in ~/tmp. Sort out where you want your program to end up
sudo mkdir /share/apps/dalton
sudo chown $USER /share/apps/dalton
mkdir /share/apps/dalton/bin /share/apps/dalton/basis /share/apps/dalton/lsdalton

Next,
cd ~/tmp
tar xvf Dalton2011_release_v0.tgz
cd Dalton2011_release/DALTON
./configure 

and answer all the questions:
------------------------------------------------------------------
   Configuring the DALTON Makefile.config and "dalton" run script
------------------------------------------------------------------

INFO: Operating system from 'uname -s' : Linux
INFO: Processor type   from 'uname -m' : x86_64
No architecture specified, attempting auto-configuration:
This appears to be a -linux architecture. Is this correct? [Y/n] 
--> Installing DALTON on a -linux computer


Note that 64-bit integers are desirable for Cholesky and very large
scale CI, otherwise the most important effect is that some files will be bigger.

If you choose 64-bit integers, be careful that any system library
routines (incl. MPI) also use 64-bit integers!

Do you want 64-bit integers? [y/N] Do you want to install the program in a parallel MPI version? [Y/n] 
-->WARNING: Makefiles for MPI architecture are difficult to guess
   Please compare the generated Makefile.config with local documentation.

   Checking for Fortran compiler ...
   from this list: mpif90 mpiifort ifort pgf95 pgf90 gfortran g95 

Compiler /opt/openmpi/bin/mpif90 found, use this compiler? [Y/n] 
-->Compiler mpif90 found and accepted.
Is backend compiler gfortran ? [Y/n] 
   Checking for C compiler ...
   from this list: mpicc  mpiicc   icc ecc pgcc gcc 

Compiler /opt/openmpi/bin/mpicc found, use this compiler? [Y/n] 
-->Compiler mpicc found and accepted.

Testing existence of libraries in this order:
 libacml.a libmkl.so libmkl_p3.a libatlas.a libblas.a
Directory search list for libraries:
  /state/partition1/home/me/tmp/ATLAS/build/lib /state/partition1/apps/ATLAS/lib /lib /usr/local/lib /usr/lib /usr/local/lib/ATLAS /lib64 /usr/lib64 /usr/local/lib64 

Do you want to replace this with your own directory search list? [y/N] Found /state/partition1/home/me/tmp/ATLAS/build/lib/libatlas.a, use it? [Y/n] Found /state/partition1/apps/ATLAS/lib/libatlas.a, use it? [Y/n] 
-->The following mathematical library(ies) will be used:
   -L/state/partition1/apps/ATLAS/lib -llapack -llapack -lf77blas -latlas


DALTON uses almost 100 Megabytes of static
allocations, in addition to the dynamic allocation.

DALTON has the possibility to reserve an amount of static memory
for storing two-electron integrals in direct and parallel calculations
Storing some or all of the 2-el. integrals in memory will speed up
direct and parallel calculations (and in particular the latter).
NOTE: This will increase the static memory allocation used by DALTON

Would you like to activate the possibility of storing 2-el.int. in memory? [y/N] How many MB to use for storing 2-el. integrals? 
-->Program will be installed with 500 MB (65000000 words) used for storing 2-el. integrals

Maximum amount of work memory for dynamic allocations can be changed
at run time with the environment variable WRKMEM (in REAL*8 words = megabytes/8)
or by using the -M option to the run script: "dalton -M mb ..." (in megabytes).
We recommend at least 200 MB work memory,
larger for correlated calculations, but it should for maximum
efficiency NOT exceed available physical memory per CPU in parallel calculations.

How many MB to use as default for work memory (hit return for default of 1000 MB)? 
-->Program will be installed with a default work memory of 900 MB (117000000 words)

-->Current directory is /home/me/tmp/Dalton2011_release/DALTON

Use default ../bin as installation directory for DALTON binaries and scripts? [Y/n] Please enter another installation directory: 
-->DALTON executable and script will be placed in /share/apps/dalton/test directory


-->Default basis set directory will be /home/me/tmp/Dalton2011_release/DALTON/../basis/

Use this directory as default basis set directory? [Y/n] 
Please choose another default basis set directory (must end with /) 
-->Default basis set directory will be /share/apps/dalton/basis/


I did not find /work, /scratch, /scr, or /temp. I will use /tmp

-->Job specific directories under $SCRATCH/$USER
-->will be used for temporary files when running DALTON

Use SCRATCH=/tmp as default root scratch space in "dalton" run script? [Y/n] 
-->Creating Makefile.config ...
gfortran version 412 prc=x86_64
INFO: Compiling with 32-bit integers.
INFO: Make sure pre-compiled BLAS, MPI etc. libraries are also with 32-bit integers!!!

Proper 64-bit file access detected.

-->Creating the DALTON run-script in /share/apps/dalton/test

   The configuration of DALTON has finished succesfully.
   Check compiler flags etc. in Makefile.config and run "make" to get executable.

Regardless of what you'll answer, here's an example of a Makefile.config that I used. The key is to add -I../modules to INCLUDES, and delete -fbacktrace.


ARCH        = linux
#
#
CPPFLAGS      = -DVAR_GFORTRAN -DSYS_LINUX -DVAR_MFDS -D'INSTALL_WRKMEM=117000000' -D'INSTALL_MMWORK=65000000' -D_FILE_OFFSET_BITS=64 -DVAR_MPI -DGFORTRAN=412 -DIMPLICIT_NONE
F90           = mpif90
CC            = mpicc
LOADER        = mpif90
RM            = rm -f
FFLAGS        = -march=x86-64 -O3 -ffast-math -funroll-loops -ftree-vectorize 
SAFEFFLAGS    = -march=x86-64 -O3 -ffast-math -funroll-loops -ftree-vectorize 
CFLAGS        = -march=x86-64 -O3 -ffast-math -funroll-loops -ftree-vectorize -std=c99 -DRESTRICT=restrict -DFUNDERSCORE=1
INCLUDES      = -I../include -I../modules
MODULES       = -J../modules
LIBS          = -L/state/partition1/apps/ATLAS/lib -llapack -llapack -lf77blas -latlas -L/opt/openmpi/lib -lmpi
INSTALLDIR    = /share/apps/dalton/test
PDPACK_EXTRAS = linpack.o eispack.o gp_zlapack.o gp_dlapack.o
GP_EXTRAS     = 
AR            = ar
ARFLAGS       = rvs
# flags for ftnchek on Dalton /hjaaj
CHEKFLAGS  = -nopure -nopretty -nocommon -nousage -noarray -notruncation -quiet  -noargumants -arguments=number  -usage=var-unitialized
# -usage=var-unitialized:arg-const-modified:arg-alias
# -usage=var-unitialized:var-set-unused:arg-unused:arg-const-modified:arg-alias
#
default : dalton linuxparallel.x
SAFE_FFLAGS_for_ifort = $(FFLAGS)
#
# Parallel initialization
#
MPI_INCLUDE_DIR = 
MPI_LIB_PATH    = 
MPI_LIB         = 
#
#
# Suffix rules
# hjaaj Oct 04: .g is a "cheat" suffix, for debugging.
#               'make x.g' will create x.o from x.F or x.c with -g debug flag set.
#
.SUFFIXES : .F .F90 .c .o .i .g .s

.F.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F 

.F.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F > $*.i

.F.g:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(SAFEFFLAGS) -g -c $*.F 

.F.s:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -S -g -c $*.F 

.F90.o:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -c $*.F90 

.F90.i:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) -E $*.F90 > $*.i

.F90.g:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(SAFEFFLAGS) -g -c $*.F90 

.F90.s:
        $(F90) $(INCLUDES) $(MODULES) $(CPPFLAGS) $(FFLAGS) -S -g -c $*.F90 

.c.o:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -c $*.c 

.c.i:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -E $*.c > $*.i

.c.g:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -g -c $*.c 

.c.s:
        $(CC) $(INCLUDES) $(CPPFLAGS) $(CFLAGS) -S -g -c $*.c 

 
If all is looking well, make.
make
cd ../
cp basis/* /share/apps/dalton/basis

DO NOT RUN MAKE IN PARALLEL i.e. no make -j3 or anything like that.
Add /share/apps/dalton/bin to your PATH i.e. add a line saying
export PATH=$PATH:/share/apps/dalton/bin
to your ~/.bashrc and source it.
So far I haven't had much time to look at it, but here's the result of the 'short' test series:
./TEST -dalton /share/apps/dalton/bin/dalton short 
[..]
#####################################################################
                              Summary
#####################################################################

THERE IS A PROBLEM IN TEST CASE(S)
 prop_exci prop_vibg2 walk_vibave2 dftmm_1
date and time         : Sun Nov  4 18:41:59 PST 2012

Here's what I found for each of the troublesome ones above:

prop_exci:
126:  INFO from READIN: Threshold for discarding integrals was    1.00D-16
127:  INFO from READIN: Threshold is reset to minimum value       1.00D-15
But otherwise it finished ok.

prop_vibg2:
 SIROUT stat info, IST and IEND =                   0                  -1
 IST or IEND out of bounds - probably no optimization in this run.
But otherwise it finished ok.

walk_vibave2:
3 informational messages have been issued by Dalton,
output from 'grep -n INFO'  (max 10 lines):
549: *** SETSIR-INFO, time in NSETUP:       0.00 seconds.
2346: *** SETSIR-INFO, time in NSETUP:       0.00 seconds.
3691: *** SETSIR-INFO, time in NSETUP:       0.00 seconds
But otherwise it finished ok.

dftmm_1:
 NOTE:    1 warnings have been issued.
 Check output, result, and error files for "WARNING".
dftmm_1.tar.gz has been copied to /home/me/tmp/Dalton2011_release/DALTON/test
----------------------------------------------------------
2 WARNINGS have been issued by Dalton,
output from 'grep -n -i WARNING'  (max 10 warnings):
711: NOTE:    1 warnings have been issued.
712: Check output, result, and error files for "WARNING".
I can't find the warning in the output, which looks like it finished ok.

All in all, it looks very promising.


Note on running in parallel
I had to do

mkdir /tmp/$USER
first.

In addition, when running I have to explicitly define my scratch directory:
dalton -t /tmp/$USER -N 4 myinput.dal myinput.mol
Other than that it's OK. I just get the overall impression that things aren't very stable (some jobs crash, some don't)

02 November 2012

274. Kernel 3.7-rc3

There's a specific driver (Silicom devices) included in the new kernel (3.7) that interests a friend. I do not suggest people in general run an -rc kernel, so I'm not going to put any effort into making this post user-friendly.

Having said that, in general you should be fine. In general.

sudo apt-get install kernel-package fakeroot build-essential
mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/testing/linux-3.7-rc3.tar.bz2
tar xvf linux-3.7-rc3.tar.bz2 
cd linux-3.7-rc3/
cat /boot/config-`uname -r`>.config
make oldconfig

At this stage you'll be asked questions about all the shiny new things that are found in the kernel. See bottom of the post for a list of the questions.

If you regret the answer to a question you can change your mind later by doing
make menuconfig

Once you're done answering questions, compile!
make-kpkg clean
time fakeroot make-kpkg -j3 --initrd --revision=3.7.0 --append-to-version=-rc3 kernel_image kernel_headers

It takes 43 minutes on my old AMD X3.



To install the kernel:
mv ../linux-*-3.7.0-rc3*.deb .
sudo dpkg -i *.deb

And you're done!

New stuff (compared to kernel 3.6.3):

* CPU/Task time and stats accounting
*
Cputime accounting
> 1. Simple tick based cputime accounting (TICK_CPU_ACCOUNTING) (NEW)
  2. Fine granularity task level IRQ time accounting (IRQ_TIME_ACCOUNTING)
choice[1-2]: 1

Consider userspace as in RCU extended quiescent state (RCU_USER_QS) [N/y/?] (NEW) 
Module signature verification (MODULE_SIG) [N/y/?] (NEW)  
Legacy cpb sysfs knob support for AMD CPUs (X86_ACPI_CPUFREQ_CPB) [Y/n/?] (NEW) 
Packet: sockets monitoring interface (PACKET_DIAG) [N/m/y/?] (NEW)
IPv6: GRE tunnel (IPV6_GRE) [N/m/y/?] (NEW) 
IPv4 NAT (NF_NAT_IPV4) [N/m/?] (NEW) 
IPv6 NAT (NF_NAT_IPV6) [N/m/?] (NEW) 
OMAP OCP2SCP DRIVER (OMAP_OCP2SCP) [N/m/y/?] (NEW) 
Maximum expected bad eraseblock count per 1024 eraseblocks (MTD_UBI_BEB_LIMIT) [20] (NEW)
UBI Fastmap (Experimental feature) (MTD_UBI_FASTMAP) [N/y/?] (NEW)
Calxeda Highbank SATA support (SATA_HIGHBANK) [N/m/?] (NEW) 
Virtual eXtensible Local Area Network (VXLAN) (VXLAN) [N/m/y/?] (NEW) Y
PCH PTP clock support (PCH_PTP) [N/y/?] (NEW)
Solarflare SFC9000-family PTP support (SFC_PTP) [Y/n/?] (NEW)
Drivers for Atheros AT803X PHYs (AT803X_PHY) [N/m/?] (NEW)
MAX310X support (SERIAL_MAX310X) [N/y/?] (NEW)
SCCNXP serial port support (SERIAL_SCCNXP) [N/m/y/?] (NEW)
TPM HW Random Number Generator support (HW_RANDOM_TPM) [M/n/?] (NEW) 
TPM Interface Specification 1.2 Interface (I2C - Infineon) (TCG_TIS_I2C_INFINEON) [N/m/?] (NEW) 
NXP SC18IS602/602B/603 I2C to SPI bridge (SPI_SC18IS602) [N/m/?] (NEW)
OMAP HDQ driver (HDQ_MASTER_OMAP) [N/m/?] (NEW)
Analog Devices ADT7410 (SENSORS_ADT7410) [N/m/?] (NEW)
Maxim MAX197 and compatibles (SENSORS_MAX197) [N/m/y/?] (NEW)
generic cpu cooling support (CPU_THERMAL) [N/y/?] (NEW) Y
Fairchild FAN53555 Regulator (REGULATOR_FAN53555) [N/m/?] (NEW)
Media USB Adapters (MEDIA_USB_SUPPORT) [N/y/?] (NEW)
Media PCI Adapters (MEDIA_PCI_SUPPORT) [N/y/?] (NEW) 
Media test drivers (V4L_TEST_DRIVERS) [N/y] (NEW) 
ISA and parallel port devices (MEDIA_PARPORT_SUPPORT) [N/y/?] (NEW) 
Autoselect tuners and i2c modules to build (MEDIA_SUBDRV_AUTOSELECT) [Y/n/?] (NEW) 
Maximum debug level (NOUVEAU_DEBUG) [5] (NEW)
Default debug level (NOUVEAU_DEBUG_DEFAULT) [3] (NEW)
Backlight Driver for LM3630 (BACKLIGHT_LM3630) [N/m/?] (NEW)
Backlight Driver for LM3639 (BACKLIGHT_LM3639) [N/m/?] (NEW)
Sony PS3 BD Remote Control (HID_PS3REMOTE) [N/m/?] (NEW)
HID Sensors framework support (HID_SENSOR_HUB) [N/m/?] (NEW)
ZTE USB serial driver (USB_SERIAL_ZTE) [N/m/?] (NEW)
Functions for loading firmware on EZUSB chips (USB_EZUSB_FX2) [M/y/?] (NEW) 
OMAP USB2 PHY Driver (OMAP_USB2) [N/m/y/?] (NEW)
LED support for LM3642 Chip (LEDS_LM3642) [N/m/?] (NEW)
LED support for LM355x Chips, LM3554 and LM3556 (LEDS_LM355x) [N/m/?] (NEW)
LED CPU Trigger (LEDS_TRIGGER_CPU) [N/y/?] (NEW)
Dallas DS2404 (RTC_DRV_DS2404) [N/m/y/?] (NEW) 
Silicom devices (NET_VENDOR_SILICOM) [Y/n/?] (NEW) Y
Silicom BypassCTL library support (SBYPASS) [N/m/?] (NEW)m
Silicom BypassCTL net support (BPCTL) [N/m/?] (NEW) m
Cambridge Electronic Design 1401 USB support (CED1401) [N/m/?] (NEW)
Digi Realport driver (DGRP) [N/m/y/?] (NEW)
STE-Modem remoteproc support (STE_MODEM_RPROC) [N/m/y/?] (NEW)
SMB2 network file system support (EXPERIMENTAL) (CIFS_SMB2) [N/y/?] (NEW)
Red-Black tree test (RBTREE_TEST) [N/m/?] (NEW)
Interval tree test (INTERVAL_TREE_TEST) [N/m/?] (NEW)
CAST5 (CAST-128) cipher algorithm (x86_64/AVX) (CRYPTO_CAST5_AVX_X86_64) [N/m/y/?] (NEW)
CAST6 (CAST-256) cipher algorithm (x86_64/AVX) (CRYPTO_CAST6_AVX_X86_64) [N/m/y/?] (NEW)
Asymmetric (public-key cryptographic) key type (ASYMMETRIC_KEY_TYPE) [N/m/y/?] (NEW)

As for Intel devices the pre-existing settings were:

Intel devices (NET_VENDOR_INTEL) [Y/n/?] y
      Intel(R) PRO/100+ support (E100) [M/n/y/?] m
      Intel(R) PRO/1000 Gigabit Ethernet support (E1000) [M/n/y/?] m
      Intel(R) PRO/1000 PCI-Express Gigabit Ethernet support (E1000E) [M/n/y/?] m
      Intel(R) 82575/82576 PCI-Express Gigabit Ethernet support (IGB) [M/n/y/?] m
        Direct Cache Access (DCA) Support (IGB_DCA) [Y/n/?] y
        PTP Hardware Clock (PHC) (IGB_PTP) [N/y/?] n
      Intel(R) 82576 Virtual Function Ethernet support (IGBVF) [M/n/y/?] m
      Intel(R) PRO/10GbE support (IXGB) [M/n/y/?] m
      Intel(R) 10GbE PCI Express adapters support (IXGBE) [M/n/y/?] m
        Intel(R) 10GbE PCI Express adapters HWMON support (IXGBE_HWMON) [Y/n/?] y
        Direct Cache Access (DCA) Support (IXGBE_DCA) [Y/n/?] y
        Data Center Bridging (DCB) Support (IXGBE_DCB) [Y/n/?] y
        PTP Clock Support (IXGBE_PTP) [N/y/?] n
      Intel(R) 82599 Virtual Function Ethernet support (IXGBEVF) [M/n/y/?] m
      Intel (82586/82593/82596) devices (NET_VENDOR_I825XX) [Y/n/?] y
        Zenith Z-Note support (EXPERIMENTAL) (ZNET) [N/m/y/?] n