bartlettroscoe
commented
8 years ago @BarrySmith , the current 'master' version of PETSc fails the download of SuperLUDist. Do you know what happened with this? See the detailed error below.
CC: @jwillenbring
Detailed Notes:
Trying to produce a static build of xSDK with xSDKTrilinos ...
I cloned the installxSDK repo with:
$ git clone git@github.com:xsdk-project/installxSDK.gitI then attempted to do the static build with:
$ ./installxSDK.sh --prefix=../install/mpi_debug_static --enable-shared=0but it got the following error in the configure of NetCDF:
checking for library containing H5Fflush... noconfigure: error: Can't find or link to the hdf5 library. Use --disable-netcdf-4, or see config.log for errors.I sent Barry and Jason an email with the detailed configure.log file.
I just realized that the configure script for PETSc that Alicia and I were using did not download and install NetCDF or ExodusII or Metis or Boost.
Barry said that the installxSDK.sh script is actaully currently cloning PETSc from bitbucket master, cloning Trilinos on the 12.6 branch and then cloning xSDKTrilinos on its master branch.
Therefore, I will go back and try doing a static build of PETSc then Trilinos, then xSDKTrilinos individually and see if I can reproduce this problem.
1) Install PETSc and TPLs with static libs:
Using PETSc on master:
$ cd PETSC_BASE=/home/8vt/localhome/PROJECTS/PETSc.base/petsc/
$ git checkout master
$ git pull
$ git log-short --name-status -1
1736e08 "Added --download-xxx-configure-arguments for passing additional configure options"
Author: Barry Smith <bsmith@mcs.anl.gov>
Date: Tue Apr 12 14:34:26 2016 -0500 (2 hours ago)
M config/BuildSystem/config/package.pyConfigure, build, and install PETSc and its TPLs:
$ export PETSC_BASE=/home/8vt/localhome/PROJECTS/PETSc.base
$ cd $PETSC_BASE/
$ cd petsc/
$ git clean -fdx
$ export PETSC_INSTALL_DIR=$PETSC_BASE/install/mpi-debug-static
$ time ./configure \
--prefix=${PETSC_INSTALL_DIR} --enable-shared=0 \
--with-cxx-dialect=C++11 --with-c++-support --with-clanguage=cxx \
--download-superlu_dist --download-hypre --download-metis --download-parmetis \
&> configure.out
real 2m5.420s
user 3m40.979s
sys 1m3.290sThis failed to configure, showing the failure:
Unable to checkout commit: v5.0.0 in repository: /localhome/8vt/PROJECTS/PETSc.base/petsc/arch-linux2-cxx-debug/externalpackages/git.superlu_dist.
Perhaps its a remote branch, if so - use: origin/v5.0.0It appears as though that tag does not exist in that git repo:
$ cd /localhome/8vt/PROJECTS/PETSc.base/petsc/arch-linux2-cxx-debug/externalpackages/git.superlu_dist
[8vt@th232 git.superlu_dist ((v4.3-p1))]$ git tag
v1
v2
v3.0
v3.1
v3.2
v3.3
v3.3-p1
v4.0
v4.0-p1
v4.0-p2
v4.0-p3
v4.1
v4.2
v4.3
v4.3-p1The remote is actually a PETSc mirror:
$ git remote -v
origin https://bitbucket.org/petsc/pkg-superlu_dist.git (fetch)
origin https://bitbucket.org/petsc/pkg-superlu_dist.git (push)I did a fetch:
$ git fetch originand it shows:
[8vt@th232 git.superlu_dist (master)]$ git ls-remote --tags
From https://bitbucket.org/petsc/pkg-superlu_dist.git
d181701f7656437fa799700461595494f1cf0d7a refs/tags/v1
4cd7e0bc4ab418fbd4e9edd299d4d5e9cf2d07df refs/tags/v2
e489440123f5ad750bd552d4f198014411d2c3b6 refs/tags/v3.0
f3b65b5bdb7ac6f05dc550dde796f7a183cd3132 refs/tags/v3.1
be7e97dc9404f5b817ca14f51f806c5b232559e9 refs/tags/v3.2
749f33d8104157767d443ff1a1d151642751486d refs/tags/v3.3
477ac4cb42240655cde9eb1e077f03af87b6c9fa refs/tags/v3.3-p1
01fcf8aed07ff59fddfec8a624a9a079dec480a4 refs/tags/v4.0
bdddaa1c55e208b48f96d6281b8713b55f836c6e refs/tags/v4.0-p1
27583c7ca1d2b1b0760a8f20033d92bf3b0163c1 refs/tags/v4.0-p2
dad206a611c05e60b3b5dd58030aae0941dc93ed refs/tags/v4.0-p3
1e387bb0c07bec2b746fd388e6c40892b608a8ef refs/tags/v4.1
c66af245f0c24df3aff80d98f58215f069dfd2a1 refs/tags/v4.2
7b6195f2dcd9383d5cf296be5d18b015d48fb977 refs/tags/v4.3
934ad8f128722c600221150ae0108f7c5b3568de refs/tags/v4.3-p1What is up with that? Why is PETSc 'master' pointing to a tag that does not even exist?
It seems this change got made 3 days ago in the commit:
commit b8a3fda2eec00bbbfad0cf0db17d1d1f04b07f29
Author: Barry Smith <bsmith@mcs.anl.gov>
Date: Sat Apr 9 19:36:18 2016 -0500
Updated to the release tarballs and commits for SuperLU and SuperLU_Dist
diff --git a/config/BuildSystem/config/packages/SuperLU_DIST.py b/config/BuildSystem/config/packages/SuperLU_DIST.py
index b01ff94..76af43e 100644
--- a/config/BuildSystem/config/packages/SuperLU_DIST.py
+++ b/config/BuildSystem/config/packages/SuperLU_DIST.py
@@ -4,9 +4,8 @@ import os
class Configure(config.package.CMakePackage):
def __init__(self, framework):
config.package.CMakePackage.__init__(self, framework)
- self.gitcommit = '892d677'
-# self.download = ['git://https://github.com/petsc/superlu_dist']
- self.download = ['git://https://github.com/xiaoyeli/superlu_dist']
+ self.gitcommit = 'v5.0.0'
+ self.download = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_5.0.0.tar.gz','git://https://github.com/xiaoyeli/superlu_dist']
self.functions = ['set_default_options_dist']
self.includes = ['superlu_ddefs.h']
self.liblist = [['libsuperlu_dist.a']]I don't understand how this works for anyone else.
BarrySmith
balay
sarich
In the below email, Jason reports that xSDKTrilinos is putting the libraries in the wrong order on the link line.
This Issue ticket is to investigate this issue and try to resolve it.
From: Jason Sarich jason.sarich@gmail.com on behalf of "Sarich, Jason J." sarich@mcs.anl.gov Date: Tuesday, April 12, 2016 at 1:41 PM To: "Smith, Barry F." bsmith@mcs.anl.gov Cc: "Xiaoye (Sherry) Li" xsli@lbl.gov, "Balay, Satish" balay@mcs.anl.gov, "Willenbring, James M" jmwille@sandia.gov, Sherry Li xiaoye@nersc.gov, "Klinvex, Alicia Marie" amklinv@sandia.gov, Lois Curfman McInnes curfman@mcs.anl.gov Subject: Re: nearing final preparations for xSDK release
I'm still having some trouble with installxSDK.sh on mira, I was able to fix a few issues, but now I'm getting a bad link line for xsdktrilinos. libpetsc.a is not added until the very end, but it depends on previous libraries (hdf5, superlu, metis, hypre, ml, etc.), see link command below.
I'm hoping somebody more familiar with cmake and the xsdktrilinos package can figure out where the library list is coming from quicker than I can. There's also a '-rdynamic' in there that I don't think will work.