[molpro-user] ARMCI test errors after compiling with GA/MPICH2, gfortran, ATLAS on Ubuntu 11.04

Gregory Magoon gmagoon at MIT.EDU
Fri Jun 10 20:26:02 BST 2011

Thanks Andy. Although this looked promising at first, it seems to give 
an error
on cn_samc_forces.test and hangs on cs2_qcitgrad_c2v.test. (For what it's
worth, one of my earlier attempts in which I was using the Ubuntu atlas 
encountered a hang on cn_samc_forces.test.) This time, I followed your example
much more closely (no lapack and same flags as you in ATLAS compile, no shared
object libraries for ATLAS, used /opt/ATLAS3.8.4 install location).

#get dependencies

sudo apt-get install mpich2
sudo apt-get install curl
sudo apt-get install gfortran
sudo apt-get install zlib1g-dev
sudo apt-get install libcr-dev

#disable CPU throttling (http://ubuntuforums.org/showthread.php?t=611084)
sudo /usr/bin/cpufreq-selector -g performance

#from atlas build directory:
#build8noLAPACK directory:
../configure --prefix=/opt/ATLAS3.8.4 -Si cputhrchk 0 -C if `which 
gfortran` -F
if '-O3 -m64 -fdefault-integer-8'
sed -i -e 's/F77_INTEGER=long/F77_INTEGER="long long"/' Make.inc
make check; make ptcheck
make time
sudo make install

#(clear old ATLAS .so and LAPACK libraries)

#compile molpro, using patch level 22

./configure -batch -gcc -gfortran -mpp -auto-ga-tcgmsg-mpich2 -instroot
/usr/local/molpro2010.1 -blaspath /opt/ATLAS3.8.4/lib

#tuning, testing
make patch #enter username, password to download token
make tuning
make quicktest
nohup make MOLPRO_OPTIONS=-n8 test > test061011.txt &
#***cn_samc_forces test fails; compare with attempt 3 where it hung on 
this job;
timing for big_lattice: 107/108

Test output:
Running job Cs_DKH10.test
Running job Cs_DKH2.test
Running job Cs_DKH2_standard.test
Running job Cs_DKH3.test
Running job Cs_DKH4.test
Running job Cs_DKH7.test
Running job Cs_DKH8.test
Running job Cs_nr.test
Running job allene_opt.test
Running job allyl_cipt2.test
Running job allyl_ls.test
Running job ar2_dk_dummy.test
Running job au2o_optdftecp1.test
Running job au2o_optdftecp2.test
Running job au2o_optecp.test
Running job aucs4k2.test
Running job b_cidft.test
Running job basisinput.test
Running job bccd_opt.test
Running job bccd_save.test
Running job benz_nlmo.test
Running job benzol_giao.test
Running job big_lattice.test
Running job br2_f12_multgem.test
Running job c2f4_cosmo.test
Running job c2h2_dfmp2.test
Running job c2h4_c1_freq.test
Running job c2h4_ccsd-f12.test
Running job c2h4_ccsdfreq.test
Running job c2h4_cosmo.test
Running job c2h4_cosmo_direct.test
Running job c2h4_d2.test
Running job c2h4_d2h.test
Running job c2h4_d2h_freq.test
Running job c2h4_ksfreq.test
Running job c2h4_lccsd.test
Running job c2h4_lccsd2.test
Running job c2h4_lccsd3.test
Running job c2h4_lmp2.test
Running job c2h4_optnum.test
Running job c2h4_prop.test
Running job c2h4o_cosmo.test
Running job c6h6_freq.test
Running job c6h6_freq_restart.test
Running job c6h6_opt.test
Running job caffeine_opt.test
Running job casvb.test
Running job casvb2.test
Running job casvb3.test
Running job ccsapt_hebe2_exdi_dcbs.test
Running job ccsapt_hebe_df_ccdisp_dcbs.test
Running job ccsapt_hebe_df_ccdisp_mcbs.test
Running job ccsapt_hebe_df_ccexdi_dcbs.test
Running job ccsapt_ne2ar_dcbs.test
Running job ccsapt_ne2ar_mcbs.test
Running job ccsapt_ne2ar_nosym_dcbs.test
Running job ccsapt_ne2ar_tdhfdisp_dcbs.test
Running job ccsapt_ne2ar_tdhfdisp_mcbs.test
Running job ccsd_f12_dipmom.test
Running job ch2_rs3.test
Running job ch2o_cosmo_rad.test
Running job ch3_cosmo.test
Running job ch3_cosmo_dft.test
Running job ch4_b2plyp.test
Running job ch4_b2plyp_df.test
Running job ch4_b2plyp_direct.test
Running job changegeom.test
Running job cl-_cosmo.test
Running job cl2_cosmo.test
Running job cl2_cosmo2.test
Running job cl2dft.test
Running job cl_cosmo.test
Running job cn_optrs2av.test
Running job cn_proj.test
Running job cn_samc_forces.test
3:3:fehler:: 1
(rank:3 hostname:kamet pid:32327):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
4:4:fehler:: 1
(rank:4 hostname:kamet pid:32328):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
5:5:fehler:: 1
(rank:5 hostname:kamet pid:32329):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
7:7:fehler:: 1
(rank:7 hostname:kamet pid:32331):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
0:0:fehler:: 1
(rank:0 hostname:kamet pid:32324):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
1:1:fehler:: 1
(rank:1 hostname:kamet pid:32325):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
2:2:fehler:: 1
(rank:2 hostname:kamet pid:32326):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0
6:6:fehler:: 1
(rank:6 hostname:kamet pid:32330):ARMCI DASSERT fail.
src/armci.c:ARMCI_Error():276 cond:0

=   EXIT CODE: 256
**** PROBLEMS WITH JOB cn_samc_forces.test
**** For further information, look in the output file
**** /home/user/Molpro/testjobs/cn_samc_forces.errout
Running job cn_tranh.test
Running job cn_uno.test
Running job cndft.test
Running job co2_mp2freq.test
Running job co2_vci_pmp.test
Running job co_cordip.test
Running job co_qcidip.test
Running job contest_lih2_D0D1.test
Running job coreocc.test
Running job cpp.test
Running job cppopt.test
Running job cr2_ecp_forces.test
Running job cs2_qcitgrad_c2v.test

Quoting Andy May <MayAJ1 at cardiff.ac.uk>:

> Greg,
> I can now only think the problems relate to the MPICH2 binaries or GA 
> install. I have made an updated Molpro tarball, 
> molpro.2010.1.22.tar.gz. Please can you build atlas without the 
> lapack routines, i.e.:
> # build ATLAS and install in /opt/atlas/3.8.4
> mkdir -p /tmp/ATLAS/build
> tar -C /tmp/ATLAS -xjf ~/atlas3.8.4.tar.bz2
> cd /tmp/ATLAS/build
> /tmp/ATLAS/ATLAS/configure --prefix=/opt/atlas/3.8.4 -Si cputhrchk 0 
> -C if `which gfortran` -F if '-O3 -m64 -fdefault-integer-8'
> sed -i -e 's/F77_INTEGER=long/F77_INTEGER="long long"/' Make.inc
> make
> make check
> make ptcheck
> sudo make install
> and then for Molpro, use the auto-build options which will build 
> MPICH2 from scratch and automatically build GA. Also, with this 
> tarball the extra lapack routines are all automatically compiled 
> within Molpro if ATLAS is detected.
> tar -xzf ~/molpro.2010.1.22.tar.gz
> cd Molpro
> ./configure -batch -gcc -gfortran -mpp -auto-ga-tcgmsg-mpich2 
> -instroot /usr/local/molpro2010.1 -blaspath /opt/atlas/3.8.4/lib
> For me, this gave a working build. I haven't run all of the testjobs, 
> but at least the first few of the ones where you saw problems, and 
> they worked here.
> There is one disadvantage to the above way of building, 'make 
> install' will not then work for Molpro. This is because the MPICH2 
> install can not simply be copied since some of the install 
> directories are hard-coded into the executable. We have a bug open to 
> fix this eventually. The configure script does print out exactly how 
> it is building MPICH2 and GA, so if everything works you can simply 
> build the packages as per-configure, but change the install directory 
> to some global location, eg. /opt or /usr/local and then build Molpro 
> pointing to these installs instead.
> Best wishes,
> Andy

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