Hi Pavel, I downloaded the last released version of phenix (phenix-1.9-1692) and I would like to run the "feature enhanced map" command. However, when I run it I got the following Memory Error that I didn't have in the previous version of phenix. r_work: 0.1867 r_free: 0.2372 Max B subtracted from atoms and used to sharpen map: 20.0 b_sharp: 25.0 FEM loop: done so far: 10%Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 120, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 99, in run sharp=params.sharp, signal_threshold=params.signal_threshold) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 112, in __init__ progress_counter = progress_counter) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 204, in fem_loop weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 276, in fem_loop_ weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 234, in one_iteration m = get_map(mc=mc_wa, cg=crystal_gridding) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 20, in get_map fourier_coefficients = mc) File "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", line 4357, in __init__ conjugate_flag=True) MemoryError My OS is Ubuntu precise 12.04 LTS, system 32 bit Thanks in advance Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structural J. P. Ebel 6, rue Jules Horowitz F-38027 GRENOBLE Cedex 1
Hi Matteo, I'm sorry about the problem! I afraid there are only solution two solutions: 1) use a computer with more memory: the error below tells the program needed more memory than your computer has, or 2) wait for a one of upcoming nightly builds. Since the release I've already made a number of changes that should help free some memory: for example, I switched from 1/4. to 1/3 gridding, which should significantly reduce the memory consumption (and speed up the calculations too). Pavel On 5/14/14, 1:44 AM, Matteo Colombo wrote:
Hi Pavel, I downloaded the last released version of phenix (phenix-1.9-1692) and I would like to run the "feature enhanced map" command.
However, when I run it I got the following Memory Error that I didn't have in the previous version of phenix.
r_work: 0.1867 r_free: 0.2372 Max B subtracted from atoms and used to sharpen map: 20.0 b_sharp: 25.0 FEM loop: done so far: 10%Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 120, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 99, in run sharp=params.sharp, signal_threshold=params.signal_threshold) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 112, in __init__ progress_counter = progress_counter) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 204, in fem_loop weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 276, in fem_loop_ weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 234, in one_iteration m = get_map(mc=mc_wa, cg=crystal_gridding) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 20, in get_map fourier_coefficients = mc) File "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", line 4357, in __init__ conjugate_flag=True) MemoryError
My OS is Ubuntu precise 12.04 LTS, system 32 bit
Thanks in advance
Matteo
-- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structural J. P. Ebel 6, rue Jules Horowitz F-38027 GRENOBLE Cedex 1
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On Wed, May 14, 2014 at 1:44 AM, Matteo Colombo wrote: My OS is Ubuntu precise 12.04 LTS, system 32 bit One note of caution: if you are running a 32-bit architecture or OS,
upgrading the memory may not help, because it will be limited in how much
it can address at once. (I forget if the limit is 2GB or 4GB; it may be
OS-dependent.) At this point I would recommend using 64-bit for everything
if possible, and especially not purchasing any systems that are 32-bit
only. (Are these even sold any more?)
-Nat
4 Gb is the limit of addressable memory for 32-bit machines. The amount of usable memory (RAM) is anywhere from around 2-3 Gbyte depending on hardware configuration. Some hardware (e.g., a graphics card) reserves memory space for itself, decreasing the amount available for usable RAM. I believe all relatively modern (last 5-10 years?) CPUs are 64-bit capable. A 64-bit machine should be able to address 16 Gbyte of memory. (Minus hardware deductions for usuable memory space.) Cheers, _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected] On 5/14/2014 11:05 AM, Nathaniel Echols wrote:
On Wed, May 14, 2014 at 1:44 AM, Matteo Colombo
mailto:[email protected]> wrote: My OS is Ubuntu precise 12.04 LTS, system 32 bit
One note of caution: if you are running a 32-bit architecture or OS, upgrading the memory may not help, because it will be limited in how much it can address at once. (I forget if the limit is 2GB or 4GB; it may be OS-dependent.) At this point I would recommend using 64-bit for everything if possible, and especially not purchasing any systems that are 32-bit only. (Are these even sold any more?)
-Nat
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Hi Roger, not quite 16GB: 32 bit gives 2^ 32 / 1024^3 GB = 4 GB 64 bit: 2^64 / 1024^3 = 17179869184 GB = 16 Exa B Cheers, Tim On 05/14/2014 05:13 PM, Roger Rowlett wrote:
4 Gb is the limit of addressable memory for 32-bit machines. The amount of usable memory (RAM) is anywhere from around 2-3 Gbyte depending on hardware configuration. Some hardware (e.g., a graphics card) reserves memory space for itself, decreasing the amount available for usable RAM.
I believe all relatively modern (last 5-10 years?) CPUs are 64-bit capable. A 64-bit machine should be able to address 16 Gbyte of memory. (Minus hardware deductions for usuable memory space.)
Cheers,
_______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346
tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected]
On 5/14/2014 11:05 AM, Nathaniel Echols wrote:
On Wed, May 14, 2014 at 1:44 AM, Matteo Colombo
mailto:[email protected]> wrote: My OS is Ubuntu precise 12.04 LTS, system 32 bit
One note of caution: if you are running a 32-bit architecture or OS, upgrading the memory may not help, because it will be limited in how much it can address at once. (I forget if the limit is 2GB or 4GB; it may be OS-dependent.) At this point I would recommend using 64-bit for everything if possible, and especially not purchasing any systems that are 32-bit only. (Are these even sold any more?)
-Nat
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-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Yes, a 64 bit machine can address an incredible amount of memory... If all 64 addressing lines are brought out of the CPU chip. The chips (and motherboards) I'm aware of never do. It is just not cost effective since most people can't afford exabytes of RAM. Most desktop systems are limited to 16GB but you can get some motherboards with 32GB capability. I built a desktop system with 32GB last summer for about $2000. Servers are designed to hold more memory, at a much greater cost. It was the same story for 32 bit computers. The VAX 11/780 I worded on as a PhD student was 32 bit but could only address 4MB of RAM. The lab could only afford to buy that much late in my PhD work. Dale Tronrud On 5/14/2014 9:14 AM, Tim Gruene wrote:
Hi Roger,
not quite 16GB:
32 bit gives 2^ 32 / 1024^3 GB = 4 GB 64 bit: 2^64 / 1024^3 = 17179869184 GB = 16 Exa B
Cheers, Tim
On 05/14/2014 05:13 PM, Roger Rowlett wrote:
4 Gb is the limit of addressable memory for 32-bit machines. The amount of usable memory (RAM) is anywhere from around 2-3 Gbyte depending on hardware configuration. Some hardware (e.g., a graphics card) reserves memory space for itself, decreasing the amount available for usable RAM.
I believe all relatively modern (last 5-10 years?) CPUs are 64-bit capable. A 64-bit machine should be able to address 16 Gbyte of memory. (Minus hardware deductions for usuable memory space.)
Cheers,
_______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346
tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected]
On 5/14/2014 11:05 AM, Nathaniel Echols wrote:
On Wed, May 14, 2014 at 1:44 AM, Matteo Colombo
mailto:[email protected]> wrote: My OS is Ubuntu precise 12.04 LTS, system 32 bit
One note of caution: if you are running a 32-bit architecture or OS, upgrading the memory may not help, because it will be limited in how much it can address at once. (I forget if the limit is 2GB or 4GB; it may be OS-dependent.) At this point I would recommend using 64-bit for everything if possible, and especially not purchasing any systems that are 32-bit only. (Are these even sold any more?)
-Nat
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participants (6)
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Dale Tronrud
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Matteo Colombo
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Nathaniel Echols
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Pavel Afonine
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Roger Rowlett
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Tim Gruene