April 2013 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Satish Balay 11 Apr '13

11 Apr '13

On Thu, 11 Apr 2013, Matthew Knepley wrote: > On Thu, Apr 11, 2013 at 9:38 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > On Thu, 11 Apr 2013, Matthew Knepley wrote: > > > > > On Thu, Apr 11, 2013 at 9:17 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > > > > > On Thu, 11 Apr 2013, Matthew Knepley wrote: > > > > > > > > > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> > > wrote: > > > > > > > > > > > How do we handle these packages with complicated dependencies [they > > > > > > are complicated as petsc dependencies?] > > > > > > > > > > > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > > > > > > does petsc configure automatically detect this? > > > > > > > > > > > > And I've recently used the following for hdf5/necddf5 on fusion > > [with > > > > > > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 > > from > > > > > > within configure] > > > > > > > > > > > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl > > -lhdf5 > > > > > > -lgpfs', > > > > > > > > > > > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff > > > > > > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 > > > > -lk5crypto > > > > > > -lcom_err -lidn -lssl -lcrypto -lz', > > > > > > > > > > > > Yeah - things work if the user knows the dependencies and the link > > > > > > command for those dependencies - and specify it to petsc configure > > as > > > > > > above. But I'm not sure how to autodetect this. > > > > > > > > > > > > Also currently -lz is handled in package.py with > > > > > > 'self.needsCompression' similar to 'self.needsMath' with the > > detection > > > > > > of -lz in libraires.py:checkCompression() - but one can't specify a > > > > > > --with-zlib-lib option this way. I guess this part can be fixed by > > > > > > migrating it a standalone package z.py. [And somehow handle the > > > > > > optional part of this dependency for hdf5] > > > > > > > > > > > > > > > We already have a mechanism for this. Lots of packages depend on > > > > > other packages. This is just screwed up in the case of libz because > > > > > someone (maybe me) did not want to write an entire package file for > > > > > it, and instead copped out with the needsCompression. > > > > > > > > Currently we handle 'mandatory' dependencies properly - and optional > > > > >depencencies for --download-pakcage somewhat - but not for > > > > --with-package-dir > > > > > > > > For hdf5 - handling just zlib.py is not sufficient. Do we add szip.py, > > > > zlib.py, gpfs.py [and perhaps more] for hdf5? And somehow use these as > > > > optionaly when testing for user provided --with-hdf5? Which package > > > > currently implements this usage [to check for this optionaly > > > > dependency - and give the correct error]? > > > > > > > > i.e In this case - when the user specified --with-hdf5-dir option. We > > > > had to print an error.: > > > > * please provide --with-zlib-dir and --with-szip-dir options. > > > > [For a different user - with the same usage - there would be no error] > > > > > > > > For netcdf above one would have kerbros.py, curl.py and perhaps more? > > > > > > > > > We have had this same discussion a million times, and we always > > eventually > > > get to the same answer and forget. Do we need our own error message for > > > petsc-dev? > > > > > > We cannot possibly guess everything that can go wrong. What we need is a > > > system > > > where the user can specify what he actually wants and we check it. So, > > zlib > > > and > > > everything else are optional dependencies for hdf5. If something is not > > > specified, it > > > fails, and the user goes back and specifies the right thing. > > > > Sure - but specify how? specify everything with > > --with-hdf5-lib,--with-hdf5-include options? > > > > Or somehow he knows that he has to specify > > --with-zlib-include/-with-zlib-lib options? > > > > This. It would be nice if HDF5 would tell us about its dependencies, but if > it does not, then > the user has to, and this is our system (packages). So we would start adding zlib.py, szip.py and manymore [and support --download-zlib --download-szip]. And if user gets the error: --with-hdf5-dir=/foo/bar does not work. So he/she send us configure.log Then we look at it and respond saying: you need to specify --with-zlib-dir --with-szip-dir options aswell. Does this look right? Satish > > Matt > > > > This thread started becasue one expected --with-hdf5-dir to be > > sufficient - and its not. current workarround [becuase of > > self.needsCompression] is to specify zlib with LIBS otpions - and all > > other dependencies with --with-hdf5-lib. It works - but if were were > > satisfactory - this whole thread on petsc-dev wouldn't arise. > > > > Satish > > > > > >

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Matthew Knepley 11 Apr '13

11 Apr '13

On Thu, Apr 11, 2013 at 9:38 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > On Thu, 11 Apr 2013, Matthew Knepley wrote: > > > On Thu, Apr 11, 2013 at 9:17 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > > > On Thu, 11 Apr 2013, Matthew Knepley wrote: > > > > > > > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> > wrote: > > > > > > > > > How do we handle these packages with complicated dependencies [they > > > > > are complicated as petsc dependencies?] > > > > > > > > > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > > > > > does petsc configure automatically detect this? > > > > > > > > > > And I've recently used the following for hdf5/necddf5 on fusion > [with > > > > > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 > from > > > > > within configure] > > > > > > > > > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl > -lhdf5 > > > > > -lgpfs', > > > > > > > > > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff > > > > > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 > > > -lk5crypto > > > > > -lcom_err -lidn -lssl -lcrypto -lz', > > > > > > > > > > Yeah - things work if the user knows the dependencies and the link > > > > > command for those dependencies - and specify it to petsc configure > as > > > > > above. But I'm not sure how to autodetect this. > > > > > > > > > > Also currently -lz is handled in package.py with > > > > > 'self.needsCompression' similar to 'self.needsMath' with the > detection > > > > > of -lz in libraires.py:checkCompression() - but one can't specify a > > > > > --with-zlib-lib option this way. I guess this part can be fixed by > > > > > migrating it a standalone package z.py. [And somehow handle the > > > > > optional part of this dependency for hdf5] > > > > > > > > > > > > We already have a mechanism for this. Lots of packages depend on > > > > other packages. This is just screwed up in the case of libz because > > > > someone (maybe me) did not want to write an entire package file for > > > > it, and instead copped out with the needsCompression. > > > > > > Currently we handle 'mandatory' dependencies properly - and optional > > > >depencencies for --download-pakcage somewhat - but not for > > > --with-package-dir > > > > > > For hdf5 - handling just zlib.py is not sufficient. Do we add szip.py, > > > zlib.py, gpfs.py [and perhaps more] for hdf5? And somehow use these as > > > optionaly when testing for user provided --with-hdf5? Which package > > > currently implements this usage [to check for this optionaly > > > dependency - and give the correct error]? > > > > > > i.e In this case - when the user specified --with-hdf5-dir option. We > > > had to print an error.: > > > * please provide --with-zlib-dir and --with-szip-dir options. > > > [For a different user - with the same usage - there would be no error] > > > > > > For netcdf above one would have kerbros.py, curl.py and perhaps more? > > > > > > We have had this same discussion a million times, and we always > eventually > > get to the same answer and forget. Do we need our own error message for > > petsc-dev? > > > > We cannot possibly guess everything that can go wrong. What we need is a > > system > > where the user can specify what he actually wants and we check it. So, > zlib > > and > > everything else are optional dependencies for hdf5. If something is not > > specified, it > > fails, and the user goes back and specifies the right thing. > > Sure - but specify how? specify everything with > --with-hdf5-lib,--with-hdf5-include options? > > Or somehow he knows that he has to specify > --with-zlib-include/-with-zlib-lib options? > This. It would be nice if HDF5 would tell us about its dependencies, but if it does not, then the user has to, and this is our system (packages). Matt > This thread started becasue one expected --with-hdf5-dir to be > sufficient - and its not. current workarround [becuase of > self.needsCompression] is to specify zlib with LIBS otpions - and all > other dependencies with --with-hdf5-lib. It works - but if were were > satisfactory - this whole thread on petsc-dev wouldn't arise. > > Satish > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Satish Balay 11 Apr '13

11 Apr '13

On Thu, 11 Apr 2013, Matthew Knepley wrote: > On Thu, Apr 11, 2013 at 9:17 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > On Thu, 11 Apr 2013, Matthew Knepley wrote: > > > > > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > > > > > How do we handle these packages with complicated dependencies [they > > > > are complicated as petsc dependencies?] > > > > > > > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > > > > does petsc configure automatically detect this? > > > > > > > > And I've recently used the following for hdf5/necddf5 on fusion [with > > > > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 from > > > > within configure] > > > > > > > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl -lhdf5 > > > > -lgpfs', > > > > > > > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff > > > > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 > > -lk5crypto > > > > -lcom_err -lidn -lssl -lcrypto -lz', > > > > > > > > Yeah - things work if the user knows the dependencies and the link > > > > command for those dependencies - and specify it to petsc configure as > > > > above. But I'm not sure how to autodetect this. > > > > > > > > Also currently -lz is handled in package.py with > > > > 'self.needsCompression' similar to 'self.needsMath' with the detection > > > > of -lz in libraires.py:checkCompression() - but one can't specify a > > > > --with-zlib-lib option this way. I guess this part can be fixed by > > > > migrating it a standalone package z.py. [And somehow handle the > > > > optional part of this dependency for hdf5] > > > > > > > > > We already have a mechanism for this. Lots of packages depend on > > > other packages. This is just screwed up in the case of libz because > > > someone (maybe me) did not want to write an entire package file for > > > it, and instead copped out with the needsCompression. > > > > Currently we handle 'mandatory' dependencies properly - and optional > > >depencencies for --download-pakcage somewhat - but not for > > --with-package-dir > > > > For hdf5 - handling just zlib.py is not sufficient. Do we add szip.py, > > zlib.py, gpfs.py [and perhaps more] for hdf5? And somehow use these as > > optionaly when testing for user provided --with-hdf5? Which package > > currently implements this usage [to check for this optionaly > > dependency - and give the correct error]? > > > > i.e In this case - when the user specified --with-hdf5-dir option. We > > had to print an error.: > > * please provide --with-zlib-dir and --with-szip-dir options. > > [For a different user - with the same usage - there would be no error] > > > > For netcdf above one would have kerbros.py, curl.py and perhaps more? > > > We have had this same discussion a million times, and we always eventually > get to the same answer and forget. Do we need our own error message for > petsc-dev? > > We cannot possibly guess everything that can go wrong. What we need is a > system > where the user can specify what he actually wants and we check it. So, zlib > and > everything else are optional dependencies for hdf5. If something is not > specified, it > fails, and the user goes back and specifies the right thing. Sure - but specify how? specify everything with --with-hdf5-lib,--with-hdf5-include options? Or somehow he knows that he has to specify --with-zlib-include/-with-zlib-lib options? This thread started becasue one expected --with-hdf5-dir to be sufficient - and its not. current workarround [becuase of self.needsCompression] is to specify zlib with LIBS otpions - and all other dependencies with --with-hdf5-lib. It works - but if were were satisfactory - this whole thread on petsc-dev wouldn't arise. Satish

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Matthew Knepley 11 Apr '13

11 Apr '13

On Thu, Apr 11, 2013 at 9:17 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > On Thu, 11 Apr 2013, Matthew Knepley wrote: > > > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > > > How do we handle these packages with complicated dependencies [they > > > are complicated as petsc dependencies?] > > > > > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > > > does petsc configure automatically detect this? > > > > > > And I've recently used the following for hdf5/necddf5 on fusion [with > > > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 from > > > within configure] > > > > > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl -lhdf5 > > > -lgpfs', > > > > > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff > > > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 > -lk5crypto > > > -lcom_err -lidn -lssl -lcrypto -lz', > > > > > > Yeah - things work if the user knows the dependencies and the link > > > command for those dependencies - and specify it to petsc configure as > > > above. But I'm not sure how to autodetect this. > > > > > > Also currently -lz is handled in package.py with > > > 'self.needsCompression' similar to 'self.needsMath' with the detection > > > of -lz in libraires.py:checkCompression() - but one can't specify a > > > --with-zlib-lib option this way. I guess this part can be fixed by > > > migrating it a standalone package z.py. [And somehow handle the > > > optional part of this dependency for hdf5] > > > > > > We already have a mechanism for this. Lots of packages depend on > > other packages. This is just screwed up in the case of libz because > > someone (maybe me) did not want to write an entire package file for > > it, and instead copped out with the needsCompression. > > Currently we handle 'mandatory' dependencies properly - and optional > >depencencies for --download-pakcage somewhat - but not for > --with-package-dir > > For hdf5 - handling just zlib.py is not sufficient. Do we add szip.py, > zlib.py, gpfs.py [and perhaps more] for hdf5? And somehow use these as > optionaly when testing for user provided --with-hdf5? Which package > currently implements this usage [to check for this optionaly > dependency - and give the correct error]? > > i.e In this case - when the user specified --with-hdf5-dir option. We > had to print an error.: > * please provide --with-zlib-dir and --with-szip-dir options. > [For a different user - with the same usage - there would be no error] > > For netcdf above one would have kerbros.py, curl.py and perhaps more? We have had this same discussion a million times, and we always eventually get to the same answer and forget. Do we need our own error message for petsc-dev? We cannot possibly guess everything that can go wrong. What we need is a system where the user can specify what he actually wants and we check it. So, zlib and everything else are optional dependencies for hdf5. If something is not specified, it fails, and the user goes back and specifies the right thing. Matt > > Satish > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Satish Balay 11 Apr '13

11 Apr '13

On Thu, 11 Apr 2013, Matthew Knepley wrote: > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > How do we handle these packages with complicated dependencies [they > > are complicated as petsc dependencies?] > > > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > > does petsc configure automatically detect this? > > > > And I've recently used the following for hdf5/necddf5 on fusion [with > > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 from > > within configure] > > > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl -lhdf5 > > -lgpfs', > > > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff > > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto > > -lcom_err -lidn -lssl -lcrypto -lz', > > > > Yeah - things work if the user knows the dependencies and the link > > command for those dependencies - and specify it to petsc configure as > > above. But I'm not sure how to autodetect this. > > > > Also currently -lz is handled in package.py with > > 'self.needsCompression' similar to 'self.needsMath' with the detection > > of -lz in libraires.py:checkCompression() - but one can't specify a > > --with-zlib-lib option this way. I guess this part can be fixed by > > migrating it a standalone package z.py. [And somehow handle the > > optional part of this dependency for hdf5] > > > We already have a mechanism for this. Lots of packages depend on > other packages. This is just screwed up in the case of libz because > someone (maybe me) did not want to write an entire package file for > it, and instead copped out with the needsCompression. Currently we handle 'mandatory' dependencies properly - and optional >depencencies for --download-pakcage somewhat - but not for --with-package-dir For hdf5 - handling just zlib.py is not sufficient. Do we add szip.py, zlib.py, gpfs.py [and perhaps more] for hdf5? And somehow use these as optionaly when testing for user provided --with-hdf5? Which package currently implements this usage [to check for this optionaly dependency - and give the correct error]? i.e In this case - when the user specified --with-hdf5-dir option. We had to print an error.: * please provide --with-zlib-dir and --with-szip-dir options. [For a different user - with the same usage - there would be no error] For netcdf above one would have kerbros.py, curl.py and perhaps more? Satish

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Barry Smith 11 Apr '13

11 Apr '13

Entire package time :-( On Apr 11, 2013, at 7:02 AM, Matthew Knepley <knepley(a)gmail.com> wrote: > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > How do we handle these packages with complicated dependencies [they > are complicated as petsc dependencies?] > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > does petsc configure automatically detect this? > > And I've recently used the following for hdf5/necddf5 on fusion [with > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 from > within configure] > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl -lhdf5 -lgpfs', > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz', > > Yeah - things work if the user knows the dependencies and the link > command for those dependencies - and specify it to petsc configure as > above. But I'm not sure how to autodetect this. > > Also currently -lz is handled in package.py with > 'self.needsCompression' similar to 'self.needsMath' with the detection > of -lz in libraires.py:checkCompression() - but one can't specify a > --with-zlib-lib option this way. I guess this part can be fixed by > migrating it a standalone package z.py. [And somehow handle the > optional part of this dependency for hdf5] > > We already have a mechanism for this. Lots of packages depend on other packages. This is > just screwed up in the case of libz because someone (maybe me) did not want to write an > entire package file for it, and instead copped out with the needsCompression. > > Matt > > > Satish > > On Wed, 10 Apr 2013, Barry Smith wrote: > > > > > Shouldn't this be fixed by now in PETSc-dev? > > > > > > > > Begin forwarded message: > > > > > From: Satish Balay <balay(a)mcs.anl.gov> > > > Subject: Re: [petsc-users] cannot find 'libz.a' when configuring > > > Date: April 10, 2013 5:21:38 PM CDT > > > To: PETSc users list <petsc-users(a)mcs.anl.gov> > > > Reply-To: PETSc users list <petsc-users(a)mcs.anl.gov> > > > > > > try using configure option LIBS="-L/opt/zlib-1.2.7/lib -lz' > > > > > > Satish > > > > > > On Wed, 10 Apr 2013, Seungbum Koo wrote: > > > > > >> Hi. I tried to add hdf5 when configuring. HDF5-1.8.9 is currently installed > > >> with szip-2.1 and zlib-1.2.7. > > >> > > >> It stops with message > > >> > > >> ******************************************************************************* > > >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > >> details): > > >> ------------------------------------------------------------------------------- > > >> Compression library [libz.a or equivalent] not found > > >> ******************************************************************************* > > >> > > >> What I don't understand is that 'libz.a' file exists in > > >> '/opt/zlib-1.2.7/lib'. What should I do? > > >> > > >> Seungbum > > >> > > > > > > > > > > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Matthew Knepley 11 Apr '13

11 Apr '13

On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > How do we handle these packages with complicated dependencies [they > are complicated as petsc dependencies?] > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how > does petsc configure automatically detect this? > > And I've recently used the following for hdf5/necddf5 on fusion [with > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 from > within configure] > > '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl -lhdf5 > -lgpfs', > > '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto > -lcom_err -lidn -lssl -lcrypto -lz', > > Yeah - things work if the user knows the dependencies and the link > command for those dependencies - and specify it to petsc configure as > above. But I'm not sure how to autodetect this. > > Also currently -lz is handled in package.py with > 'self.needsCompression' similar to 'self.needsMath' with the detection > of -lz in libraires.py:checkCompression() - but one can't specify a > --with-zlib-lib option this way. I guess this part can be fixed by > migrating it a standalone package z.py. [And somehow handle the > optional part of this dependency for hdf5] We already have a mechanism for this. Lots of packages depend on other packages. This is just screwed up in the case of libz because someone (maybe me) did not want to write an entire package file for it, and instead copped out with the needsCompression. Matt > > Satish > > On Wed, 10 Apr 2013, Barry Smith wrote: > > > > > Shouldn't this be fixed by now in PETSc-dev? > > > > > > > > Begin forwarded message: > > > > > From: Satish Balay <balay(a)mcs.anl.gov> > > > Subject: Re: [petsc-users] cannot find 'libz.a' when configuring > > > Date: April 10, 2013 5:21:38 PM CDT > > > To: PETSc users list <petsc-users(a)mcs.anl.gov> > > > Reply-To: PETSc users list <petsc-users(a)mcs.anl.gov> > > > > > > try using configure option LIBS="-L/opt/zlib-1.2.7/lib -lz' > > > > > > Satish > > > > > > On Wed, 10 Apr 2013, Seungbum Koo wrote: > > > > > >> Hi. I tried to add hdf5 when configuring. HDF5-1.8.9 is currently > installed > > >> with szip-2.1 and zlib-1.2.7. > > >> > > >> It stops with message > > >> > > >> > ******************************************************************************* > > >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for > > >> details): > > >> > ------------------------------------------------------------------------------- > > >> Compression library [libz.a or equivalent] not found > > >> > ******************************************************************************* > > >> > > >> What I don't understand is that 'libz.a' file exists in > > >> '/opt/zlib-1.2.7/lib'. What should I do? > > >> > > >> Seungbum > > >> > > > > > > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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Re: [petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Satish Balay 10 Apr '13

10 Apr '13

How do we handle these packages with complicated dependencies [they are complicated as petsc dependencies?] In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So how does petsc configure automatically detect this? And I've recently used the following for hdf5/necddf5 on fusion [with the extra implicit depenceny of hdf5 on zlib, and netcdf5 on hdf5 from within configure] '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl -lhdf5 -lgpfs', '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib -lnetcdff -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz', Yeah - things work if the user knows the dependencies and the link command for those dependencies - and specify it to petsc configure as above. But I'm not sure how to autodetect this. Also currently -lz is handled in package.py with 'self.needsCompression' similar to 'self.needsMath' with the detection of -lz in libraires.py:checkCompression() - but one can't specify a --with-zlib-lib option this way. I guess this part can be fixed by migrating it a standalone package z.py. [And somehow handle the optional part of this dependency for hdf5] Satish On Wed, 10 Apr 2013, Barry Smith wrote: > > Shouldn't this be fixed by now in PETSc-dev? > > > > Begin forwarded message: > > > From: Satish Balay <balay(a)mcs.anl.gov> > > Subject: Re: [petsc-users] cannot find 'libz.a' when configuring > > Date: April 10, 2013 5:21:38 PM CDT > > To: PETSc users list <petsc-users(a)mcs.anl.gov> > > Reply-To: PETSc users list <petsc-users(a)mcs.anl.gov> > > > > try using configure option LIBS="-L/opt/zlib-1.2.7/lib -lz' > > > > Satish > > > > On Wed, 10 Apr 2013, Seungbum Koo wrote: > > > >> Hi. I tried to add hdf5 when configuring. HDF5-1.8.9 is currently installed > >> with szip-2.1 and zlib-1.2.7. > >> > >> It stops with message > >> > >> ******************************************************************************* > >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > >> details): > >> ------------------------------------------------------------------------------- > >> Compression library [libz.a or equivalent] not found > >> ******************************************************************************* > >> > >> What I don't understand is that 'libz.a' file exists in > >> '/opt/zlib-1.2.7/lib'. What should I do? > >> > >> Seungbum > >> > > > >

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Fwd: [petsc-users] cannot find 'libz.a' when configuring
by Barry Smith 10 Apr '13

10 Apr '13

Shouldn't this be fixed by now in PETSc-dev? Begin forwarded message: > From: Satish Balay <balay(a)mcs.anl.gov> > Subject: Re: [petsc-users] cannot find 'libz.a' when configuring > Date: April 10, 2013 5:21:38 PM CDT > To: PETSc users list <petsc-users(a)mcs.anl.gov> > Reply-To: PETSc users list <petsc-users(a)mcs.anl.gov> > > try using configure option LIBS="-L/opt/zlib-1.2.7/lib -lz' > > Satish > > On Wed, 10 Apr 2013, Seungbum Koo wrote: > >> Hi. I tried to add hdf5 when configuring. HDF5-1.8.9 is currently installed >> with szip-2.1 and zlib-1.2.7. >> >> It stops with message >> >> ******************************************************************************* >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for >> details): >> ------------------------------------------------------------------------------- >> Compression library [libz.a or equivalent] not found >> ******************************************************************************* >> >> What I don't understand is that 'libz.a' file exists in >> '/opt/zlib-1.2.7/lib'. What should I do? >> >> Seungbum >> >

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Re: [petsc-dev] examples/benchmarks for weak and strong scaling exercise
by Nystrom, William D 10 Apr '13

10 Apr '13

Sorry. I overlooked that the URL was using git protocol. My bad. Dave ________________________________________ From: Jed Brown [five9a2(a)gmail.com] on behalf of Jed Brown [jedbrown(a)mcs.anl.gov] Sent: Wednesday, April 10, 2013 12:10 PM To: Nystrom, William D; For users of the development version of PETSc; Chris Kees Subject: Re: [petsc-dev] examples/benchmarks for weak and strong scaling exercise "Nystrom, William D" <wdn(a)lanl.gov> writes: > Jed, > > I tried cloning your tme-ice git repo as follows and it failed: > > % git clone --recursive git://github.com/jedbrown/tme-ice.git tme_ice > Cloning into 'tme_ice'... > fatal: unable to connect to github.com: > github.com[0: 204.232.175.90]: errno=Connection timed out > > I'm doing this from an xterm that allows me to clone petsc just fine. You're using https or ssh to clone PETSc, but the git:// to clone tme-ice. The LANL network is blocking that port, so just use the https or ssh protocol.

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