hdfeos5 @1.13r2 Configure failure

[uthyr@…]

Hi,

system info: Xserve hardware, running Mac OS X Server 10.6.8, with all Software Update patches applied.

my primary command that led to this configure failure was: "sudo port install ncarg +gcc45". I explicitly install the following ports in the following order, to build a foundation for a few packages along with ncarg/ncl:

wget +ssl
db46
gcc45
python27 (followed by the python_select command)
ghostscript
gv +letter
ImageMagick +q16
gsl +gcc45
hdf5-18 +cxx +gcc45 (have also tried this with "hdf5-18 +cxx +gcc45 +szip")
hdf4 +gcc45
netcdf +dap +netcdf4 +hdf4
netcdf-fortran +gcc45
nco
ncarg +gcc45

in building the dependencies for ncarg, I now repeatedly get the "configure failure" for hdfeos5. I've tried "sudo port clean hdfeos5", then "sudo port install hdfeos5" and also "sudo port install hdfeos5 +szip". all attempts fail currently.

Installation of this same group of packages worked recently, I believe it was last week, on my Lion machine. My list of outdated ports on the Lion machine show upgrades available for:

automake 1.12.2_0 < 1.12.4_0
bison 2.6_0 < 2.6.2_0
cairo 1.12.2_0 < 1.12.2_1
cctools 822_2 < 829_1
cctools-headers 822_2 < 829_0
curl 7.26.0_0 < 7.27.0_1
curl-ca-bundle 7.26.0_1 < 7.27.0_0
fftw-3 3.3.2_0 < 3.3.2_1
gcc45 4.5.4_1 < 4.5.4_6
gcc_select 0.1_6 < 0.1_7
gdal 1.9.0_3 < 1.9.1_1
ghostscript 9.05_2 < 9.06_1
gmp 5.0.4_1 < 5.0.5_0
gsl 1.15_1 < 1.15_2
hdf4 4.2.7_0 < 4.2.7_1
hdf5-18 1.8.9_0 < 1.8.9_2
ImageMagick 6.7.8-3_0 < 6.7.9-0_2
lcms2 2.3_0 < 2.4_0
ld64 128.2_4 < 133.3_3
lftp 4.3.5_0 < 4.3.8_0
libmpc 1.0_0 < 1.0.1_0
libpng 1.4.12_0 < 1.5.12_0
libtool 2.4.2_2 < 2.4.2_3
libxml2 2.7.8_0 < 2.8.0_0
llvm-3.1 3.1_1 < 3.1_3
mesa 8.0.4_0 < 8.0.4_1
ncarg 6.0.0_5 < 6.0.0_10
nco 4.2.0_0 < 4.2.1_1
netcdf-fortran 4.2_4 < 4.2_5
netpbm 10.59.00_0 < 10.59.00_1
pkgconfig 0.27_0 < 0.27.1_1
sqlite3 3.7.13_0 < 3.7.14_1
tcl 8.5.11_0 < 8.5.12_1
webp 0.1.3_0 < 0.2.0_1
wget 1.13.4_0 < 1.14_0
wgrib2 1.9.6a_0 < 1.9.6a_3

The only change I've made in the package requests since the Lion install last week (or so) is that hdf5-18 did not have "+cxx" as a default then. At that time, hdfeos5 @1.13r2 configured, built and installed fine.

please check, and thanks for all your work with these packages!

[ryandesign (Ryan Carsten Schmidt)]

Please attach the main.log from the failed installation.

[uthyr@…]

hdfeos5 log

[uthyr@…]

ncarg log

[uthyr@…]

Replying to ryandesign@…:

Please attach the main.log from the failed installation.

now attached - thanks!

[gnw3]

The relevant section of hdfeos5.main.log is:

455     :info:configure checking for gcc... /opt/local/bin/h5cc
456	:info:configure checking for C compiler default output file name...
457	:info:configure configure: error: C compiler cannot create executables
458	:info:configure See `config.log' for more details.

You might want to look at h5cc to see why it is failing.

[tenomoto (Takeshi Enomoto)]

Could you upload config.log of hdfeos5?

[uthyr@…]

hdfeos5 config log

[uthyr@…]

Replying to takeshi@…:

Could you upload config.log of hdfeos5?

sorry for the delay. hdfeos5 config.log now uploaded.

[uthyr@…]

I just looked at the hdfeos web page (​http://hdfeos.org/software/hdfeos.php), and found a mention of indicating that hdfeos5 requires use of the hdf5 version 1.6 API. The hdf5-18 port is installed, and I was wondering if the CFLAGS definition for "H5_USE_16_API" was being used for hdfeos5...

here is the potentially relevant text from the hdfeos web page:

"The first step is to execute configure script included in the package. One option is required as a parameter to configure: CC. If HDF5 is 1.8 or higher, one needs to define H5_USE_16_API preprocessor macro as CFLAGS. This is because HDF-EOS5 uses HDF5 1.6 API and this is not compatible with HDF5 1.8 API. If HDF5 was built with SZIP, another option --with-szlib is required. The following is an example when HDF5 1.8 is built with SZIP."

and the sample code block immediately following on the web page is:

$ ./configure \
CC=<hdf5_path>/bin/h5cc \
CFLAGS=-DH5_USE_16_API \
--with-szlib=<szip_path>

[tenomoto (Takeshi Enomoto)]

We have configure.cflags-append -DH5_USE_16_API in Portfile.

I looked at config.log. h5cc calls MacPorts' gcc-mp-4.5. Can your gcc-mp-4.5 or h5cc compile hello, world? I have XServe running Snow Leopard Server at work it uses the default gcc-4.2 h5cc is just a shell script.

CCBASE="/usr/bin/gcc-4.2"
CLINKERBASE="/usr/bin/gcc-4.2"

[jmroot (Joshua Root)]

The problem seems to be that it calls h5cc with -arch x86_64, when h5cc is backed by a non-apple gcc.

[uthyr@…]

I had this same issue on one of our Mac Pro computers, running 10.6.8, with Xcode 3.6.2 installed.

same problem, with h5cc calling /opt/local/bin/gcc-mp-4.5, apparently unable to compile executables.

To me this is odd, as 2 of my 8 Mac Pros went through the process of "selfupdate", and "upgrade outdated" without any hitches or changes to package files, while 1 of the 8 exhibited the problem I've found on one of my Xserve computers.

on the problematic Mac Pro, I modified the lines in /opt/local/bin/h5cc to:

CCBASE="/usr/bin/gcc-4.2"
CLINKERBASE="/usr/bin/gcc-4.2"

This did not solve the issue.

I then modified them further, to:

CCBASE="/Developer/usr/bin/gcc-4.2"
CLINKERBASE="/Developer/usr/bin/gcc-4.2"

and then the hdfeos5 package compiled and installed completely!

MacPorts found 4 broken ports (wgrib2, ImageMagick, vis5d, and ncarg), which it then repaired. There was an issue with the ncarg install, which was resolved after running the "port clean ncarg" command.

However, when I applied a similar procedure on my Xserve, trying both the paths for gcc-4.2 (with and without the /Developer prefix), I had no success.

I will be proceeding though the other 5 Mac Pros, and gathering more statistics on my issues with this port.

thanks, Roy

[uthyr@…]

Replying to uthyr@…:

However, when I applied a similar procedure on my Xserve, trying both the paths for gcc-4.2 (with and without the /Developer prefix), I had no success.

aha - the problem now on the Xserve was that I hadn't specified that hdfeos5 be built with szip, and it was specified for hdf5! once I specified

sudo port install hdfeos5 +szip

the hdfeos5 package built completely!

so, it appears the solution for my issues were that I needed to use the Developer gcc-4.2 compiler to compile hdfeos5 on some of my 10.6.8 computers.

I believe this ticket may be closed, as I think I can get the rest of my Mac Pros and Xserve updated now.

thank you all for your assistance, Roy

[tenomoto (Takeshi Enomoto)]

I was able to reproduce the problem. I fixed it by unsetting archflags. Committed in r101449.