error: relocation truncated to fit, additional relocation overflows omitted from the output

The recommended flags to use when you have >2GB of static data are:
-mcmodel medium -shared-intel
or

-mcmodel large -shared-intel
(>>2GB)

Make the SGE jobs rerunnable automatically

qconf -mq all.q

and set

rerun                 TRUE

job for Antares3

#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -pe orte 24


. /share/apps/intel/bin/ifortvars.sh intel64
. /share/apps/intel/impi/4.0.3.008/bin64/mpivars.sh


/share/apps/intel/impi/4.0.3.008/bin64/mpiexec.hydra -bootstrap sge /share/apps/SIESTA/3.1/siesta  < Au411.fdf

/etc/exports

/export 10.1.1.1(rw,async,no_root_squash) 10.1.0.0/255.255.0.0(rw,async)
/state/partition1 10.1.1.1(rw,async,no_root_squash) 10.1.0.0/255.255.0.0(rw,async)
/export/home 10.1.1.1(rw,async,no_root_squash) 10.1.0.0/255.255.0.0(rw,async)
/share  10.1.1.1(rw,async,no_root_squash) 10.1.0.0/255.255.0.0(rw,async)

Send files from command line

mandar un archivo:

uuencode surfing.jpeg surfing.jpeg | mail sylvia@home.com

Un directorio
tar cvf - panda | uuencode panda.tar | mail whoever@whatever.com 

tar zcvf - *psf MoS2-wire.out ds5b_30atms.DM ds5b_30atms.XV 
ds5b_30atms.STRUCT_NEXT_ITER  ds5b_30atms.STRUCT_OUT | uuencode MoS2.pseudo.tgz 
| mail quevedin@gmail.com 

Job Ranger

#!/bin/bash
#$ -V # Inherit the submission environment
#$ -cwd # Start job in submission directory
#$ -N MoS2-crushed # Job Name
#$ -j y # Combine stderr and stdout
#$ -o $JOB_NAME.o$JOB_ID # Name of the output file (eg. myMPI.oJobID)
#$ -pe 16way 16 # Requests 16 tasks/node, 32 cores total
#$ -q normal # Queue name "normal"
#$ -A MoS2_Nanocatalysts
#$ -l h_rt=24:00:00 # Run time (hh:mm:ss) - 1.5 hours
#$ -M quevedin+ranger@gmail.com # Use email notification address
#$ -m be # Email at Begin and End of job
#module swap pgi intel/9.1
module load pgi/8.0-6
#/8.0-6pintel/9.1
#module swap mvapich openmpi
#module load openmpi/1.2.4
export GFORTRAN_UNBUFFERED_ALL=1
set -x # Echo commands, use "set echo" with csh
if [ -f MoS2-wire.out ]; then refecha MoS2-wire.out; fi
if [ -f *.ANI ]; then for i in *.ANI ; do refechacp  $i; done; fi
ibrun ~/SIESTA/siesta-3.1/Obj-pgi/siesta < MoS2-wire.final.crushed.fdf | tee MoS2-wire.final.crushed.out # Run the MPI executable named "a.out"

compute-0-3

falla de nuevo, probablemente hay que hacer una melange de piezas

Extract version from RCS

co -r1 /etc/gmond.conf
see diffs:
rcsdiff /etc/gmond.conf
or
diff -r1.2 /etc/gmond.conf

convertir posiciones

for i in `seq 562 1000`; do j=$((i-1)); tail -n $i $i.TXT > $i.tmp; echo "$i.tmp $j" |./convierte.x > $j.xyz; rm $i.tmp ; done


for i in 75 76 77 78; do for j in A B C; do if [ -f $i$j ]; then echo "$i$j $i" | ./convierte.x > $i$j.xyz; fi; done; done

Premios Nobel

He encontrado este gran Artículo del blog de Physics Today. Que lo disfrutéis.

Limpiar el .bash_history a lo burro

history | sort +1 | uniq -f 1 | sort -n| cut -c 8- > .bash_history.nodups

echar un vistazo que todo esté bien y luego mover a .bash_history

Qué quiere decir ZP en Newsweek

The awful truth: la gráfica que nadie te pintará (porque hay que saber hacer un sumatorio, ni siquiera integrar)

Faster dd

dd if=/dev/sdc1 conv=noerror,sync bs=64k | dd of=/dev/sdi1 bs=64k
9856+0 registros de entrada
9855+0 registros de salida
645857280 bytes (646 MB) copiados, 17,871 s, 36,1 MB/s

frente a

dd if=/dev/sdc1 of=/dev/sdi1
3801513+0 registros de entrada
3801513+0 registros de salida
1946374656 bytes (1,9 GB) copiados, 1055,21 s, 1,8 MB/s

Quitar archivos sobrantes de SIESTA

rm $(find . -name "CHLOCAL.*" -or -name "KB.L*" -or -name "ORB.S*" -or -name "*.ion*" -or -name "*.POT.CONF" -or -name "VNA.*" -or -name "RED_VLOCAL.*" -or -name "INPUT_TMP.*" | head -2000)

No Kylie, No

PWSCF

$PW_COMMAND < si.scf.in > si.scf.out

$PW_COMMAND < si.band.in > si.band.out

$PLOTBAND_COMMAND < si.plotband.in > si.plotband.out
(plotband.x)

momentos magneticos

grep -A170 "mulliken: Atomic and Orbital Populations:" parallel.output | grep -v '^$' | grep -v Atom | grep -v 4pz> spins.dat
awk 'NR % 3 == 1' spins.dat

scp alias

in .bashrc:

function mn1 { scp $1 user@machine.dom: ;}

($1, $2... argumentos en linea de comando)
o

function mn1 { scp $* user@machine.dom: ;}

(pa que meta todo)
# mn1 cosa1
Password:

GFORTRAN buffer issues

export GFORTRAN_UNBUFFERED_ALL=1
(it kills the buffer)

check-swap.sh

#!/bin/bash
if grep -q "/swap" /etc/fstab
then
echo "Encontrado"
else
echo "Añadiendo"
echo '/swap swap swap defaults 0 0' >> /etc/fstab
mount -a
fi