Hi Andrew, We ran the install script from scratch, so I assume it would have installed the version of cython it needed? Elizabeth On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:

Hi Elizabeth,

I saw errors like this when I tried to use an older version of Cython. Are you sure that you're using version 0.16?

-Andrew M

On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker wrote: Hi,

We've had some problems installing yt via the install script.

Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with:

cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c

Error compiling Cython file: ------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) v_dir = malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:393:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... cdef np.float64_t px, py cdef np.float64_t width[3] for i in range(3): width[i] = self.width[i] if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:364:32: Invalid value for num_threads argument, expected an int error: 3 errors while compiling 'yt/utilities/lib/grid_traversal.pyx' with Cython

Has anyone had a similar experience?

Elizabeth _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi Nathan, This is also a mac - but I'll suggest we update gcc. Thanks! Elizabeth On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:

Hi Elizabeth,

I tried running the install script on my mac laptop after your e-mail. I was able to build yt from the install script with no problems.

It would help if you could let us know a bit more about the system you're trying to build yt on. In particular, I think you'll run into issues if you're using an old version of gcc that doesn't support OpenMP. Version 4.2 or newer should work.

-Nathan

On 7/13/12 12:16 AM, Elizabeth Tasker wrote:

...

Hi Andrew,

We ran the install script from scratch, so I assume it would have installed the version of cython it needed?

Elizabeth

On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:

...

Hi Elizabeth,

I saw errors like this when I tried to use an older version of Cython. Are you sure that you're using version 0.16?

-Andrew M

On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker mailto:tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi,

We've had some problems installing yt via the install script.

Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with:

cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c

Error compiling Cython file: ------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) v_dir = malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:393:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... cdef np.float64_t px, py cdef np.float64_t width[3] for i in range(3): width[i] = self.width[i] if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:364:32: Invalid value for num_threads argument, expected an int error: 3 errors while compiling 'yt/utilities/lib/grid_traversal.pyx' with Cython

Has anyone had a similar experience?

Elizabeth _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac compilers, but they don't support many Darwin specific flags, causing common build systems to break. This took way too long to figure out as a new Mac user. Much better to stick with Xcode gcc and get the AT&T research gfortran. If you really want a new version of gnu compilers (kind of amazing how far behind they are), I think macports has newer versions built to have the apple flags. - Casey On Friday, July 13, 2012, Sam Skillman wrote:

Beware -- updating gcc to anything past 4.2 will likely break the compile on a mac. You want to make sure to use the Xcode gcc, which you should be able to do by setting:

export CC=gcc-4.2 export CXX=g++-4.2

or the equivaltent command in csh if you aren't a bash person. If you had done that, then I'm not sure what the problem would be. You'll likely have to wipe the existing install for those exports to do you any good.

Sam

On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker < tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi Nathan,

This is also a mac - but I'll suggest we update gcc. Thanks!

Elizabeth

On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:

...

Hi Elizabeth,

I tried running the install script on my mac laptop after your e-mail. I was able to build yt from the install script with no problems.

It would help if you could let us know a bit more about the system you're trying to build yt on. In particular, I think you'll run into issues if you're using an old version of gcc that doesn't support OpenMP. Version 4.2 or newer should work.

-Nathan

On 7/13/12 12:16 AM, Elizabeth Tasker wrote:

...

Hi Andrew,

We ran the install script from scratch, so I assume it would have installed the version of cython it needed?

Elizabeth

On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:

...

Hi Elizabeth,

I saw errors like this when I tried to use an older version of Cython. Are you sure that you're using version 0.16?

-Andrew M

On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker < tasker@astro1.sci.hokudai.ac.jp mailto:tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi,

We've had some problems installing yt via the install script.

Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with:

cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c

Error compiling Cython file: ------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) v_dir = malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^

I'm +1 on making things more explicit in the install_script message to users (particularly of mac). I think most people treat it like a black box and hope for the best. And if it breaks they come here. If something popped up and said, *make sure you have xcode gcc installed*, it might be better for all involved. Cameron On 07/13/2012 11:38 AM, Matthew Turk wrote:

Hi Casey,

Thanks for the summary of the options -- perhaps we should make the warning more explicit in the install_script?

With respect to things being far behind, I think the situation will only get worse. Apple stopped updating gcc when they moved to GPLv3, and have started shipping their own stack based on LLVM. Perhaps a brainstorming session of options -- the Xcode gcc, AT&T research gfortran, Macports, other binary installers, etc etc -- would be helpful over on yt-dev for addressing how to keep up to date with GCC as well as ensure compatibility with as much as possible.

-Matt

On Fri, Jul 13, 2012 at 8:17 AM, Casey W. Stark wrote:

...

That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac compilers, but they don't support many Darwin specific flags, causing common build systems to break. This took way too long to figure out as a new Mac user. Much better to stick with Xcode gcc and get the AT&T research gfortran.

If you really want a new version of gnu compilers (kind of amazing how far behind they are), I think macports has newer versions built to have the apple flags.

- Casey

On Friday, July 13, 2012, Sam Skillman wrote:

...

Beware -- updating gcc to anything past 4.2 will likely break the compile on a mac. You want to make sure to use the Xcode gcc, which you should be able to do by setting:

export CC=gcc-4.2 export CXX=g++-4.2

or the equivaltent command in csh if you aren't a bash person. If you had done that, then I'm not sure what the problem would be. You'll likely have to wipe the existing install for those exports to do you any good.

Sam

On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker wrote:

Hi Nathan,

This is also a mac - but I'll suggest we update gcc. Thanks!

Elizabeth

On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:

...

Hi Elizabeth,

I tried running the install script on my mac laptop after your e-mail. I was able to build yt from the install script with no problems.

It would help if you could let us know a bit more about the system you're trying to build yt on. In particular, I think you'll run into issues if you're using an old version of gcc that doesn't support OpenMP. Version 4.2 or newer should work.

-Nathan

On 7/13/12 12:16 AM, Elizabeth Tasker wrote:

...

Hi Andrew,

We ran the install script from scratch, so I assume it would have installed the version of cython it needed?

Elizabeth

On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:

...

Hi Elizabeth,

I saw errors like this when I tried to use an older version of Cython. Are you sure that you're using version 0.16?

-Andrew M

On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker mailto:tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi,

We've had some problems installing yt via the install script.

Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with:

cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c

Error compiling Cython file: ------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) v_dir = malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- Cameron Hummels PhD Candidate, Astronomy Department of Columbia University Public Outreach Director, Astronomy Department of Columbia University NASA IYA New York State Student Ambassador http://outreach.astro.columbia.edu PGP: 0x06F886E3

Is it actually true that yt still works with the xcode gcc from 10.5? I though that compiler didn't support openmp, which is now required. -Andrew M On Fri, Jul 13, 2012 at 8:53 AM, Sam Skillman wrote:

Here's what the install script current spits out:

Looks like you're running on Mac OSX.

NOTE: you must have the Xcode command line tools installed.

OS X 10.5: download Xcode 3.0 from the mac developer tools website

OS X 10.6: download Xcode 3.2 from the mac developer tools website

OS X 10.7: download Xcode 4.0 from the mac app store or alternatively download the Xcode command line tools from the mac developer tools website

NOTE: You may have problems if you are running OSX 10.6 (Snow Leopard) or newer. If you do, please set the following environment variables, remove any broken installation tree, and re-run this script verbatim.

$ export CC=gcc-4.2 $ export CXX=g++-4.2

On Fri, Jul 13, 2012 at 9:48 AM, Cameron Hummels < chummels@astro.columbia.edu> wrote:

...

I'm +1 on making things more explicit in the install_script message to users (particularly of mac). I think most people treat it like a black box and hope for the best. And if it breaks they come here. If something popped up and said, *make sure you have xcode gcc installed*, it might be better for all involved.

Cameron

On 07/13/2012 11:38 AM, Matthew Turk wrote:

...

Hi Casey,

Thanks for the summary of the options -- perhaps we should make the warning more explicit in the install_script?

With respect to things being far behind, I think the situation will only get worse. Apple stopped updating gcc when they moved to GPLv3, and have started shipping their own stack based on LLVM. Perhaps a brainstorming session of options -- the Xcode gcc, AT&T research gfortran, Macports, other binary installers, etc etc -- would be helpful over on yt-dev for addressing how to keep up to date with GCC as well as ensure compatibility with as much as possible.

-Matt

On Fri, Jul 13, 2012 at 8:17 AM, Casey W. Stark wrote:

...

That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac compilers, but they don't support many Darwin specific flags, causing common build systems to break. This took way too long to figure out as a new Mac user. Much better to stick with Xcode gcc and get the AT&T research gfortran.

If you really want a new version of gnu compilers (kind of amazing how far behind they are), I think macports has newer versions built to have the apple flags.

- Casey

On Friday, July 13, 2012, Sam Skillman wrote:

...

Beware -- updating gcc to anything past 4.2 will likely break the compile on a mac. You want to make sure to use the Xcode gcc, which you should be able to do by setting:

export CC=gcc-4.2 export CXX=g++-4.2

or the equivaltent command in csh if you aren't a bash person. If you had done that, then I'm not sure what the problem would be. You'll likely have to wipe the existing install for those exports to do you any good.

Sam

On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker > wrote:

Hi Nathan,

This is also a mac - but I'll suggest we update gcc. Thanks!

Elizabeth

On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:

Hi Elizabeth,

...

I tried running the install script on my mac laptop after your e-mail. I was able to build yt from the install script with no problems.

It would help if you could let us know a bit more about the system you're trying to build yt on. In particular, I think you'll run into issues if you're using an old version of gcc that doesn't support OpenMP. Version 4.2 or newer should work.

-Nathan

On 7/13/12 12:16 AM, Elizabeth Tasker wrote:

> Hi Andrew, > > We ran the install script from scratch, so I assume it would have > installed the version of cython it needed? > > Elizabeth > > > On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote: > > Hi Elizabeth, >> >> I saw errors like this when I tried to use an older version of >> Cython. >> Are you sure that you're using version 0.16? >> >> -Andrew M >> >> On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker >> > tasker@astro1.sci.**hokudai.ac.jp >> >> >> wrote: >> >> Hi, >> >> We've had some problems installing yt via the install script. >> >> Initially it did not download distribute, which we did by hand. >> Then, it couldn't get pip, so I commented that line out and now >> it's died on cython with: >> >> >> >> cythonc:> yt/utilities/lib/**PointsInVolume.c >> building extension "yt.utilities.lib.QuadTree" sources >> cythonc:> yt/utilities/lib/QuadTree.c >> building extension "yt.utilities.lib.**RayIntegrators" sources >> cythonc:> yt/utilities/lib/**RayIntegrators.c >> building extension "yt.utilities.lib.**VolumeIntegrator" >> sources >> cythonc:> yt/utilities/lib/**VolumeIntegrator.c >> building extension "yt.utilities.lib.grid_**traversal" sources >> cythonc:> yt/utilities/lib/grid_**traversal.c >> >> Error compiling Cython file: >> ------------------------------**------------------------------ >> ... >> if im.vd_strides[0] == -1: >> with nogil, parallel(num_threads = num_threads): >> idata = >> malloc(sizeof(**ImageAccumulator)) >> idata.supp_data = self.supp_data >> v_pos = malloc(3 * >> sizeof(np.float64_t)) >> for j in prange(size, >> schedule="static",chunksize=1)**: >> ^ >> ------------------------------**------------------------------ >> >> yt/utilities/lib/grid_**traversal.pyx:368:31: Invalid keyword >> argument: chunksize >> >> Error compiling Cython file: >> ------------------------------**------------------------------ >> ... >> idata.supp_data = self.supp_data >> v_pos = malloc(3 * >> sizeof(np.float64_t)) >> v_dir = malloc(3 * >> sizeof(np.float64_t)) >> # If we do not have a simple image plane, we >> have >> to cast all >> # our rays >> for j in prange(size, schedule="dynamic", >> chunksize=100): >> ^ >> >

______________________________**_________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

______________________________**_________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

-- Cameron Hummels PhD Candidate, Astronomy Department of Columbia University Public Outreach Director, Astronomy Department of Columbia University NASA IYA New York State Student Ambassador http://outreach.astro.**columbia.edu http://outreach.astro.columbia.edu PGP: 0x06F886E3

______________________________**_________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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There's no need, 10.5 comes with GCC 4.2. On Jul 13, 2012, at 9:02 AM, Matthew Turk wrote:

On Fri, Jul 13, 2012 at 8:58 AM, Andrew Myers wrote:

...

Is it actually true that yt still works with the xcode gcc from 10.5? I though that compiler didn't support openmp, which is now required.

Hmm. We could possibly try to detect whether the -fopenmp option is available or not, but I'm not sure how to do that. This might require modifying distutils or using an env var.

...

-Andrew M

On Fri, Jul 13, 2012 at 8:53 AM, Sam Skillman wrote:

...

Here's what the install script current spits out:

Looks like you're running on Mac OSX.

NOTE: you must have the Xcode command line tools installed.

OS X 10.5: download Xcode 3.0 from the mac developer tools website

OS X 10.6: download Xcode 3.2 from the mac developer tools website

OS X 10.7: download Xcode 4.0 from the mac app store or alternatively download the Xcode command line tools from the mac developer tools website

NOTE: You may have problems if you are running OSX 10.6 (Snow Leopard) or newer. If you do, please set the following environment variables, remove any broken installation tree, and re-run this script verbatim.

$ export CC=gcc-4.2 $ export CXX=g++-4.2

On Fri, Jul 13, 2012 at 9:48 AM, Cameron Hummels wrote:

...

I'm +1 on making things more explicit in the install_script message to users (particularly of mac). I think most people treat it like a black box and hope for the best. And if it breaks they come here. If something popped up and said, *make sure you have xcode gcc installed*, it might be better for all involved.

Cameron

On 07/13/2012 11:38 AM, Matthew Turk wrote:

...

Hi Casey,

Thanks for the summary of the options -- perhaps we should make the warning more explicit in the install_script?

With respect to things being far behind, I think the situation will only get worse. Apple stopped updating gcc when they moved to GPLv3, and have started shipping their own stack based on LLVM. Perhaps a brainstorming session of options -- the Xcode gcc, AT&T research gfortran, Macports, other binary installers, etc etc -- would be helpful over on yt-dev for addressing how to keep up to date with GCC as well as ensure compatibility with as much as possible.

-Matt

On Fri, Jul 13, 2012 at 8:17 AM, Casey W. Stark wrote:

...

That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac compilers, but they don't support many Darwin specific flags, causing common build systems to break. This took way too long to figure out as a new Mac user. Much better to stick with Xcode gcc and get the AT&T research gfortran.

If you really want a new version of gnu compilers (kind of amazing how far behind they are), I think macports has newer versions built to have the apple flags.

- Casey

On Friday, July 13, 2012, Sam Skillman wrote: > > Beware -- updating gcc to anything past 4.2 will likely break the > compile > on a mac. You want to make sure to use the Xcode gcc, which you > should be > able to do by setting: > > export CC=gcc-4.2 > export CXX=g++-4.2 > > or the equivaltent command in csh if you aren't a bash person. If you > had > done that, then I'm not sure what the problem would be. You'll likely > have > to wipe the existing install for those exports to do you any good. > > Sam > > On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker > wrote: > > Hi Nathan, > > This is also a mac - but I'll suggest we update gcc. Thanks! > > Elizabeth > > > On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote: > >> Hi Elizabeth, >> >> I tried running the install script on my mac laptop after your >> e-mail. >> I was able to build yt from the install script with no problems. >> >> It would help if you could let us know a bit more about the system >> you're trying to build yt on. In particular, I think you'll run into >> issues >> if you're using an old version of gcc that doesn't support OpenMP. >> Version >> 4.2 or newer should work. >> >> -Nathan >> >> >> On 7/13/12 12:16 AM, Elizabeth Tasker wrote: >>> >>> Hi Andrew, >>> >>> We ran the install script from scratch, so I assume it would have >>> installed the version of cython it needed? >>> >>> Elizabeth >>> >>> >>> On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote: >>> >>>> Hi Elizabeth, >>>> >>>> I saw errors like this when I tried to use an older version of >>>> Cython. >>>> Are you sure that you're using version 0.16? >>>> >>>> -Andrew M >>>> >>>> On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker >>>> >>> mailto:tasker@astro1.sci.hokudai.ac.jp> >>>> wrote: >>>> >>>> Hi, >>>> >>>> We've had some problems installing yt via the install script. >>>> >>>> Initially it did not download distribute, which we did by hand. >>>> Then, it couldn't get pip, so I commented that line out and now >>>> it's died on cython with: >>>> >>>> >>>> >>>> cythonc:> yt/utilities/lib/PointsInVolume.c >>>> building extension "yt.utilities.lib.QuadTree" sources >>>> cythonc:> yt/utilities/lib/QuadTree.c >>>> building extension "yt.utilities.lib.RayIntegrators" sources >>>> cythonc:> yt/utilities/lib/RayIntegrators.c >>>> building extension "yt.utilities.lib.VolumeIntegrator" sources >>>> cythonc:> yt/utilities/lib/VolumeIntegrator.c >>>> building extension "yt.utilities.lib.grid_traversal" sources >>>> cythonc:> yt/utilities/lib/grid_traversal.c >>>> >>>> Error compiling Cython file: >>>> ------------------------------------------------------------ >>>> ... >>>> if im.vd_strides[0] == -1: >>>> with nogil, parallel(num_threads = num_threads): >>>> idata = >>>> malloc(sizeof(ImageAccumulator)) >>>> idata.supp_data = self.supp_data >>>> v_pos = malloc(3 * >>>> sizeof(np.float64_t)) >>>> for j in prange(size, >>>> schedule="static",chunksize=1): >>>> ^ >>>> ------------------------------------------------------------ >>>> >>>> yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword >>>> argument: chunksize >>>> >>>> Error compiling Cython file: >>>> ------------------------------------------------------------ >>>> ... >>>> idata.supp_data = self.supp_data >>>> v_pos = malloc(3 * >>>> sizeof(np.float64_t)) >>>> v_dir = malloc(3 * >>>> sizeof(np.float64_t)) >>>> # If we do not have a simple image plane, we >>>> have >>>> to cast all >>>> # our rays >>>> for j in prange(size, schedule="dynamic", >>>> chunksize=100): >>>> ^

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Never mind, I guess that looks explicit enough! Cameron On 07/13/2012 11:53 AM, Sam Skillman wrote:

Here's what the install script current spits out:

Looks like you're running on Mac OSX.

NOTE: you must have the Xcode command line tools installed.

OS X 10.5: download Xcode 3.0 from the mac developer tools website

OS X 10.6: download Xcode 3.2 from the mac developer tools website

OS X 10.7: download Xcode 4.0 from the mac app store or alternatively download the Xcode command line tools from the mac developer tools website

NOTE: You may have problems if you are running OSX 10.6 (Snow Leopard) or newer. If you do, please set the following environment variables, remove any broken installation tree, and re-run this script verbatim.

$ export CC=gcc-4.2 $ export CXX=g++-4.2

On Fri, Jul 13, 2012 at 9:48 AM, Cameron Hummels mailto:chummels@astro.columbia.edu> wrote:

I'm +1 on making things more explicit in the install_script message to users (particularly of mac). I think most people treat it like a black box and hope for the best. And if it breaks they come here. If something popped up and said, *make sure you have xcode gcc installed*, it might be better for all involved.

Cameron

On 07/13/2012 11:38 AM, Matthew Turk wrote:

Hi Casey,

Thanks for the summary of the options -- perhaps we should make the warning more explicit in the install_script?

With respect to things being far behind, I think the situation will only get worse. Apple stopped updating gcc when they moved to GPLv3, and have started shipping their own stack based on LLVM. Perhaps a brainstorming session of options -- the Xcode gcc, AT&T research gfortran, Macports, other binary installers, etc etc -- would be helpful over on yt-dev for addressing how to keep up to date with GCC as well as ensure compatibility with as much as possible.

-Matt

On Fri, Jul 13, 2012 at 8:17 AM, Casey W. Stark mailto:caseywstark@gmail.com> wrote:

That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac compilers, but they don't support many Darwin specific flags, causing common build systems to break. This took way too long to figure out as a new Mac user. Much better to stick with Xcode gcc and get the AT&T research gfortran.

If you really want a new version of gnu compilers (kind of amazing how far behind they are), I think macports has newer versions built to have the apple flags.

- Casey

On Friday, July 13, 2012, Sam Skillman wrote:

Beware -- updating gcc to anything past 4.2 will likely break the compile on a mac. You want to make sure to use the Xcode gcc, which you should be able to do by setting:

export CC=gcc-4.2 export CXX=g++-4.2

or the equivaltent command in csh if you aren't a bash person. If you had done that, then I'm not sure what the problem would be. You'll likely have to wipe the existing install for those exports to do you any good.

Sam

On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker mailto:tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi Nathan,

This is also a mac - but I'll suggest we update gcc. Thanks!

Elizabeth

On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:

Hi Elizabeth,

I tried running the install script on my mac laptop after your e-mail. I was able to build yt from the install script with no problems.

It would help if you could let us know a bit more about the system you're trying to build yt on. In particular, I think you'll run into issues if you're using an old version of gcc that doesn't support OpenMP. Version 4.2 or newer should work.

-Nathan

On 7/13/12 12:16 AM, Elizabeth Tasker wrote:

Hi Andrew,

We ran the install script from scratch, so I assume it would have installed the version of cython it needed?

Elizabeth

On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:

Hi Elizabeth,

I saw errors like this when I tried to use an older version of Cython. Are you sure that you're using version 0.16?

-Andrew M

On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker mailto:tasker@astro1.sci.hokudai.ac.jp mailto:tasker@astro1.sci.hokudai.ac.jp>> wrote:

Hi,

We've had some problems installing yt via the install script.

Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with:

cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c

Error compiling Cython file:

------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^

------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize

Error compiling Cython file:

------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) v_dir = malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^

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Sorry for the resend. Looks like there might be a bug in the gmail iphone app... On Fri, Jul 13, 2012 at 11:39 AM, Casey W. Stark wrote:

That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac compilers, but they don't support many Darwin specific flags, causing common build systems to break. This took way too long to figure out as a new Mac user. Much better to stick with Xcode gcc and get the AT&T research gfortran.

If you really want a new version of gnu compilers (kind of amazing how far behind they are), I think macports has newer versions built to have the apple flags.

- Casey

On Friday, July 13, 2012, Sam Skillman wrote:

...

Beware -- updating gcc to anything past 4.2 will likely break the compile on a mac. You want to make sure to use the Xcode gcc, which you should be able to do by setting:

export CC=gcc-4.2 export CXX=g++-4.2

or the equivaltent command in csh if you aren't a bash person. If you had done that, then I'm not sure what the problem would be. You'll likely have to wipe the existing install for those exports to do you any good.

Sam

On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker < tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi Nathan,

This is also a mac - but I'll suggest we update gcc. Thanks!

Elizabeth

On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:

...

Hi Elizabeth,

I tried running the install script on my mac laptop after your e-mail. I was able to build yt from the install script with no problems.

It would help if you could let us know a bit more about the system you're trying to build yt on. In particular, I think you'll run into issues if you're using an old version of gcc that doesn't support OpenMP. Version 4.2 or newer should work.

-Nathan

On 7/13/12 12:16 AM, Elizabeth Tasker wrote:

...

Hi Andrew,

We ran the install script from scratch, so I assume it would have installed the version of cython it needed?

Elizabeth

On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:

...

Hi Elizabeth,

I saw errors like this when I tried to use an older version of Cython. Are you sure that you're using version 0.16?

-Andrew M

On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker < tasker@astro1.sci.hokudai.ac.jp mailto:tasker@astro1.sci.hokudai.ac.jp> wrote:

Hi,

We've had some problems installing yt via the install script.

Initially it did not download distribute, which we did by hand. Then, it couldn't get pip, so I commented that line out and now it's died on cython with:

cythonc:> yt/utilities/lib/PointsInVolume.c building extension "yt.utilities.lib.QuadTree" sources cythonc:> yt/utilities/lib/QuadTree.c building extension "yt.utilities.lib.RayIntegrators" sources cythonc:> yt/utilities/lib/RayIntegrators.c building extension "yt.utilities.lib.VolumeIntegrator" sources cythonc:> yt/utilities/lib/VolumeIntegrator.c building extension "yt.utilities.lib.grid_traversal" sources cythonc:> yt/utilities/lib/grid_traversal.c

Error compiling Cython file: ------------------------------------------------------------ ... if im.vd_strides[0] == -1: with nogil, parallel(num_threads = num_threads): idata = malloc(sizeof(ImageAccumulator)) idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) for j in prange(size, schedule="static",chunksize=1): ^ ------------------------------------------------------------

yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword argument: chunksize

Error compiling Cython file: ------------------------------------------------------------ ... idata.supp_data = self.supp_data v_pos = malloc(3 * sizeof(np.float64_t)) v_dir = malloc(3 * sizeof(np.float64_t)) # If we do not have a simple image plane, we have to cast all # our rays for j in prange(size, schedule="dynamic", chunksize=100): ^