Rapeseed Options Explained

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Building from source : configure options explained

Packages ngs-sdk , ncbi-vdb , sra-tools have some unusual configure options.

Here we will try to explain them.

ncbi-vdb package depends on ngs-sdk , sra-tools – on ngs-sdk and ncbi-vdb .

ncbi-vdb should be able to find include files of ngs-sdk , sra-tools – ngs-sdk package and sources and build results of ncbi-vdb .

By default build output / build results of ngs / ncbi-vdb / sra-tools is created in

You can change it by using –build-prefix , but then – you should tell sra-tools where to find build results of ncbi-vdb .

Defaults: Standard / default / recommended location of source files

Default recommended locations of source files of ngs / ncbi-vdb / sra-tools is:

ngs / ncbi-vdb / sra-tools packages should be located in subdirectories named ngs , ncbi-vdb , sra-tools inside of the same directory.

Usually it is done automatically by running: git clone https://github.com/ncbi/ngs.git ; git clone https://github.com/ncbi/ncbi-vdb.git ; git clone https://github.com/ncbi/sra-tools.git

Then you should see the following:

If you create repositories as described above and run ./configure and make in each of ngs / ncbi-vdb / sra-tools subdirectories – each of them should find all required files from ngs / ncbi-vdb .

Non-standard location of ngs-sdk / ncbi-vdb

If location of ngs-sdk / ncbi-vdb or their build output directory is not standard (see above), you need to specify it:

  • ngs-sdk is in

/1/ngs-1.3.0/ngs-sdk
ncbi-vdb is in

/2/ncbi-vdb-2.8.0
sra-tools in

ncbi-vdb/configure requires to find header files of ngs-sdk :

sra-tools needs to find ngs-sdk package and ncbi-vdb ‘s sources and build results.

Configure options are sticky!

Configure options are sticky. Running configure without options will use the options that you used the last time.

./configure –with-debug # will configure with debug :)

If next time you run

./configure # it will use the same options ( same as ./configure –with-debug)

To clear the saved options and all generated files run “./configure –clear”.

To check current configuration information and options you used run:

Standard option – Install machine-independent data file’s in subdirectories of directory.

Examples of subdirectories are: bin include lib64 lib32 share

Some tools and libraries depend on third party libraries and development headers ( libxml2 , libhdf5 , . ). By default configure will attempt to utilize them from your system if they can be located.

You can provide their location by specifying one of the options: –with-hdf5-prefix , –with-xml2-prefix , etc.

Rapeseed

Rapeseed

Scientific classification
Kingdom: Plantae
Division: Magnoliophyta
Class: Magnoliopsida
Order: Capparales
Family: Brassicaceae
Genus: Brassica
Species: B. napus
Binomial name
Brassica napus
L.

Rapeseed (Brassica napus), also known as rape, oilseed rape, rapa, rapaseed and (in the case of one particular group of cultivars) canola, is a bright yellow flowering member of the family Brassicaceae (mustard or cabbage family). The name is derived from the Latin for turnip, rāpum or rāpa, and is first recorded in English at the end of the 14th century. Older writers usually distinguished the turnip and rape by the adjectives round and long(-rooted) respectively. [1] See also Brassica napobrassica, which may be considered a variety of Brassica napus. Some botanists include the closely related Brassica campestris within B. napus. (See Triangle of U)

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Cultivation and uses

Rapeseed is grown for the production of animal feed, vegetable oil for human consumption, and biodiesel; leading producers include the European Union, Canada, the United States, Australia, China and India. In India, it is grown on 13% of cropped land. According to the United States Department of Agriculture, rapeseed was the third leading source of vegetable oil in the world in 2000, after soybean and oil palm, and also the world’s second leading source of protein meal, although only one-fifth of the production of the leading soybean meal. World production is growing rapidly, with FAO reporting that 36 million tonnes of rapeseed was produced in the 2003-4 season, and 46 million tonnes in 2004-5. In Europe, rapeseed is primarily cultivated for animal feed [citation needed] (due to its very high lipid and medium protein content [citation needed] ), and is a leading option for Europeans to avoid importation of GMO products [citation needed] . Natural rapeseed oil contains erucic acid, which is mildly toxic to humans in large doses but is used as a food additive in smaller doses. Canola, originally a syncopated form of the abbreviation “Can.O., L-A.” (Canadian Oilseed, Low-Acid) that was used by the Manitoba government to label the seed during its experimental stages, is now a tradename for low erucic acid rapeseed that is sometimes mis-applied to other varieties [citation needed] .

The rapeseed is the valuable, harvested component of the crop. The crop is also grown as a winter-cover crop. It provides good coverage of the soil in winter, and limits nitrogen run-off. The plant is ploughed back in the soil or used as bedding. On some ecological or organic operations, livestock such as sheep or cattle are allowed to graze on the plants.

Processing of rapeseed for oil production provides rapeseed animal meal as a by-product. The by-product is a high-protein animal feed, competitive with soya [citation needed] . The feed is mostly employed for cattle feeding, but also for pigs and chickens (though less valuable for these). The meal has a very low content of the glucosinolates responsible for metabolism disruption in cattle and pigs [citation needed] . Rapeseed “oil cake” is also used as a fertilizer in China, and may be used for ornamentals, such as Bonsai, as well.

Rapeseed leaves and stems are also edible, similar to those of the related bok choy or kale. Some varieties of rapeseed (called 油菜, yóu cài, lit. “oil vegetable” in Chinese; yau choy in Cantonese; cải dầu in Vietnamese; and 菜の花, nanohana in Japanese) are sold as greens, primarily in Asian groceries.

Rapeseed is a heavy nectar producer, and honeybees produce a light colored, but peppery honey from it. It must be extracted immediately after processing is finished, as it will quickly granulate in the honeycomb and will be impossible to extract. The honey is usually blended with milder honeys, if used for table use, or sold as bakery grade. Rapeseed growers contract with beekeepers for the pollination of the crop.

Nutritional value

Canola oil (or rapeseed oil) contains both omega-6 and omega-3 fatty acids in a ratio of 2:1 and is second only to flax oil in omega-3 fatty acid. It is one of the most heart-healthy oils and has been reported to reduce cholesterol levels, lower serum tryglyceride levels, and keep platelets from sticking together. Some UK farmers (such as Hillfarm Oils[1]) & Farrington Oils[2]) have started to produce cold-pressed rapeseed oil as a versatile cooking oil and dressing, similar in use to olive oil.

Biodiesel

Rapeseed oil is used in the manufacture of biodiesel for powering motor vehicles. Biodiesel may be used in pure form in newer engines without engine damage, and is frequently combined with standard diesel in ratios varying from 2% to 20% biodiesel. Formerly, due to the costs of growing, crushing, and refining rapeseed biodiesel, rapeseed derived biodiesel cost more to produce than standard diesel fuel. Prices of rapeseed oil are at very high levels presently (start November 05) due to increased demand on rapeseed oil for this purpose. Rapeseed oil is the preferred oil stock for biodiesel production in most of Europe, partly because rapeseed produces more oil per unit of land area as compared to other oil sources, such as soy beans.

Rapeseed and health

Rapeseed has been linked with adverse effects in asthma and hay fever sufferers. [citation needed] Some suggest that oilseed pollen is the cause of increased breathing difficulties. [citation needed] This is unlikely however [citation needed] , as rapeseed is an entomophilous crop, with pollen transfer primarily by insects. Others suggest that it is the inhalation of oilseed rape dust that causes this [2] , and that allergies to the pollen are relatively rare. [citation needed] There may also be another effect at work; since rapeseed in flower has a distinctive and pungent smell, hay fever sufferers may wrongly jump to the conclusion that it is the rapeseed that is to blame simply because they can smell it. [citation needed] An alternative explanation may be that it is simply the sheer volume of rapeseed pollen in the air around farmland which triggers an allergic reaction in hayfever sufferers on inhalation, or following prolonged exposure to high levels.

Controversy

The Monsanto Company has genetically engineered new cultivars of rapeseed that are resistant to the effects of its herbicide Roundup. They have been vigorously prosecuting farmers found to have the Roundup Ready gene in Canola in their fields without paying a license fee [citation needed] . These farmers have claimed the Roundup Ready gene was blown into their fields and crossed with unaltered Canola [citation needed] . Other farmers claim that after spraying Roundup in non-Canola fields to kill weeds before planting, Roundup Ready volunteers are left behind, causing extra expense to rid their fields of the weeds [citation needed] .

In a closely followed legal battle, the Supreme Court of Canada found in favor of Monsanto’s patent infringement claim for illegal growing of Roundup Ready in its 2004 ruling on Monsanto Canada Inc. v. Schmeiser. The case garnered international controversy as a court-sanctioned legitimation for the global patent protection of genetically modified crops [citation needed] .

Production

Worldwide production of rapeseed (including canola) rose to 46.4 million metric tons in 2005, the highest recorded total (source: FAO).

Оптимизация запросов. Основы EXPLAIN в PostgreSQL (часть 2)

Предыдущие части:

Что происходит на физическом уровне при выполнениии нашего запроса? Разберёмся. Мой сервер поднят на Ubuntu 13.10. Используются дисковые кэши уровня ОС.
Останавливаю PostgreSQL, принудительно фиксирую изменения в файловой системе, очищаю кэши, запускаю PostgreSQL:

Теперь кэши очищены, пробуем выполнить запрос с опцией BUFFERS

QUERY PLAN
— Seq Scan on foo (cost=0.00..18334.10 rows=1000010 width=37) (actual time=0.525..734.754 rows=1000010 loops=1)
Buffers: shared read=8334
Total runtime: 1253.177 ms
(3 rows)

Таблица считывается частями — блоками. Кэш пуст. Таблица полностью считывается с диска. Для этого пришлось считать 8334 блока.
Buffers: shared read — количество блоков, считанное с диска.

Повторим последний запрос

QUERY PLAN
— Seq Scan on foo (cost=0.00..18334.10 rows=1000010 width=37) (actual time=0.173..693.000 rows=1000010 loops=1)
Buffers: shared hit=32 read=8302
Total runtime: 1208.433 ms
(3 rows)

Buffers: shared hit — количество блоков, считанных из кэша PostgreSQL.
Если повторите этот запрос несколько раз, то увидите, как PostgreSQL с каждым разом всё больше данных берёт из кэша. С каждым запросом PostgreSQL наполняет свой кэш.
Операции чтения из кэша быстрее, чем операции чтения с диска. Можете заметить эту тенденцию, отслеживая значение Total runtime .
Объём кэша определяется константой shared_buffers в файле postgresql.conf .

WHERE

Добавим в запрос условие

QUERY PLAN
— Seq Scan on foo (cost=0.00..20834.12 rows=999522 width=37)
Filter: (c1 > 500)
(2 rows)

Индексов у таблицы нет. При выполнении запроса последовательно считывается каждая запись таблицы ( Seq Scan ). Каждая запись сравнивается с условием c1 > 500 . Если условие выполняется, запись вводится в результат. Иначе — отбрасывается. Filter означает именно такое поведение.
Значение cost , что логично, увеличилось.
Ожидаемое количество строк результата — rows — уменьшилось.
В оригинале даются объяснения, почему cost принимает именно такое значение, а также каким образом рассчитывается ожидаемое количество строк.

Пора создать индексы.

QUERY PLAN
— Seq Scan on foo (cost=0.00..20834.12 rows=999519 width=37)
Filter: (c1 > 500)
(2 rows)

Ожидаемое количество строк изменилось. Уточнилось. В остальном ничего нового. Что же с индексом?

QUERY PLAN
— Seq Scan on foo (cost=0.00..20834.12 rows=999519 width=37) (actual time=0.572..848.895 rows=999500 loops=1)
Filter: (c1 > 500)
Rows Removed by Filter: 510
Total runtime: 1330.788 ms
(4 rows)

Отфильтровано только 510 строк из более чем миллиона. Пришлось считать более 99,9% таблицы.

Принудительно заставим использовать индекс, запретив Seq Scan:

QUERY PLAN
— Index Scan using foo_c1_idx on foo (cost=0.42..34623.01 rows=999519 width=37) (actual time=0.178..1018.045 rows=999500 loops=1)
Index Cond: (c1 > 500)
Total runtime: 1434.429 ms
(3 rows)

Index Scan , Index Cond вместо Filter — используется индекс foo_c1_idx .
При выборке практически всей таблицы использование индекса только увеличивает cost и время выполнения запроса. Планировщик не глуп!

Не забываем отменить запрет на использование Seq Scan:

QUERY PLAN
— Index Scan using foo_c1_idx on foo (cost=0.42..25.78 rows=491 width=37)
Index Cond: (c1 foo_c1_idx для условия c1 . Для c2

‘abcd%’::text используется фильтр.
Обратите внимание, что в выводе результатов используется POSIX формат оператора LIKE.

Если в условии только текстовое поле:

QUERY PLAN
— Seq Scan on foo (cost=0.00..20834.12 rows=100 width=37) (actual time=14.497..412.030 rows=10 loops=1)
Filter: (c2

‘abcd%’::text)
Rows Removed by Filter: 1000000
Total runtime: 412.120 ms
(4 rows)

Ожидаемо, Seq Scan .

Строим индекс по c2 :

QUERY PLAN
— Seq Scan on foo (cost=0.00..20834.12 rows=100 width=37) (actual time=20.992..424.946 rows=10 loops=1)
Filter: (c2

‘abcd%’::text)
Rows Removed by Filter: 1000000
Total runtime: 425.039 ms
(4 rows)

Опять Seq Scan ? Индекс не используется потому, что база у меня для текстовых полей использует формат UTF-8.
При создании индекса в таких случаях надо использовать класс оператора text_pattern_ops :

QUERY PLAN
— Bitmap Heap Scan on foo (cost=4.58..55.20 rows=100 width=37)
Filter: (c2

‘abcd%’::text)
-> Bitmap Index Scan on foo_c2_idx1 (cost=0.00..4.55 rows=13 width=0)
Index Cond: ((c2

‘abcd’::text) AND (c2

Bitmap Index Scan — используется индекс foo_c2_idx1 для определения нужных нам записей, а затем PostgreSQL лезет в саму таблицу: ( Bitmap Heap Scan ) -, чтобы убедиться, что эти записи на самом деле существуют. Такое поведение связано с версионностью PostgreSQL.

Если выбирать не всю строку, а только поле, по которому построен индекс

QUERY PLAN
— Index Only Scan using foo_c1_idx on foo (cost=0.42..25.78 rows=491 width=4)
Index Cond: (c1 Index Only Scan выполняется быстрее, чем Index Scan за счёт того, что не требуется читать строку таблицы полностью: width=4 .

Резюме

  • Seq Scan — читается вся таблица.
  • Index Scan — используется индекс для условий WHERE, читает таблицу при отборе строк.
  • Bitmap Index Scan — сначала Index Scan, затем контроль выборки по таблице. Эффективно для большого количества строк.
  • Index Only Scan — самый быстрый. Читается только индекс.
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